diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml index e8ace96..7716375 100644 --- a/.github/workflows/pytest.yaml +++ b/.github/workflows/pytest.yaml @@ -1,4 +1,4 @@ -name: Test with pytest and flake8 +name: Test with pytest and black on: [push] diff --git a/ccdh-pilot/README.md b/ccdh-pilot/README.md new file mode 100644 index 0000000..99ced35 --- /dev/null +++ b/ccdh-pilot/README.md @@ -0,0 +1,5 @@ +This folder contains content created for the CCDH Pilot in September 2021. + +It includes the two demonstrated developed for this Pilot as well as converters +that translate imported node data into the CRDC-H model as YAML, then validate +those transformed files using JSON Schema as well as LinkML Python data classes. diff --git a/ccdh-pilot/demonstrator-1/README.md b/ccdh-pilot/demonstrator-1/README.md new file mode 100644 index 0000000..32dc18d --- /dev/null +++ b/ccdh-pilot/demonstrator-1/README.md @@ -0,0 +1,2 @@ +Files in this directory were copied here from +https://github.com/cancerDHC/data-model-harmonization/tree/d83c2853ea6cdd8dfbb9204c2cd4c335969660c6/data-examples/f2f-2021-09-data-examples diff --git a/ccdh-pilot/demonstrator-1/d1_harmonized_gdc_specimen_cc.yaml b/ccdh-pilot/demonstrator-1/d1_harmonized_gdc_specimen_cc.yaml new file mode 100644 index 0000000..0ea0438 --- /dev/null +++ b/ccdh-pilot/demonstrator-1/d1_harmonized_gdc_specimen_cc.yaml @@ -0,0 +1,342 @@ +--- +gdc_specimen: + Title: GDC Specimen Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713cc.Specimen + Description: + - "CRDC-H-compliant representation of the 'aggregate' GDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + + Example: # type = Specimen + id: "f2f:05f1574e-2a28-50bc-bdc1-e4c6dee92fd1" # Local uuid for the Specimen a assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). +# identifier: # type = Identifier (Identifier is a complex data type, but we are only showing a single field from this type) +# - value: "target:TARGET-40-0A4I9I-01A" # GDC.Sample.sample_submitter_id (specified here as a CURIE, where the prefix indicates the system that assigned it) +# - value: "gdc-sample:9575763d-9c34-4e8e-a43a-419f5c13962f" # GDC.Sample.sample_id (specified here as a CURIE, where the prefix indicates the system that assigned it) +# - value: "biosample:SAMEA1652204" # Proposed globally unique identifier format, per recommendation of the CRDC-DST (specified here as a CURIE, where the prefix indicates the system that assigned it) + + specimen_type: # type = CodeableConcept + coding: # type = Coding + - code: C84517 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Fresh Specimen # The preferred label of the term from NCIT. + system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Sample # The second Coding holds the original code used by the source node. Here, this is the 'type' of the entity in GDC (which defines separate entities for differet types of Specimens - Sample, Portion, Aliquit, Analyte). + label: Sample # The human-readable label (implicitly the same as the code, which are human-readable in GDC) + system: http://crdc.nci.nih.gov/gdc # A URL for the GDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + associated_project: # type = ResearchProject. + id: "f2f:bc65592e-c7e2-5ab5-3c56-283ea2efc8f8" # Local uuid assigned by this system for the Research Project. The Project instance is represented separately later in this document. We will define a formal way to specify references in the next phase of work. + research_project_type: + coding: + - code: "TODO" + system: "TODO" + source_subject: # type = Subject + id: "f2f:43bcd221-80ce-508c-a7bc-7f42c31c262d" # Local uuid assigned by this system for the Subject. The Subject instance is represented separately later in this document. + source_material_type: # type = CodeableConcept (see comments on the 'specimen_type' field above for a detailed explanation of this data object's content) + coding: # type = Coding + - code: C3261 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Metastatic Neoplasm # The preferred label of the term from NCIT. + system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Metastatic # The second Coding holds the original code used by the source node. GDC uses a readable strings for their codes. + label: Metastatic # The human-readable label (implicitly the same as the code, which are human-readable in GDC) + system: http://crdc.nci.nih.gov/gdc # A URL for the GDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + general_tissue_pathology: # type = CodeableConcept + coding: # type = Coding + - code: C18009 + label: Tumor Tissue + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Tumor + label: Tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + specific_tissue_pathology: # type = CodeableConcept + coding: # type = Coding + - code: C9145 + label: Osteosarcoma + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Osteosarcoma (OS) + label: Osteosarcoma (OS) + system: http://crdc.nci.nih.gov/gdc + tag: + - original + + tumor_status_at_collection: # type = CodeableConcept + coding: # type = Coding + - code: C3261 + label: Metastatic Neoplasm + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Metastatic + label: Metastatic + system: http://crdc.nci.nih.gov/gdc + tag: + - original + +# quantity_measure: # type = QuantityMeasureObservation +# - observation_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because the weight of a specimen is captured in GDC using a dedicated property (Sample.current_weight), not as a key-vaule pair as we do here) +# coding: # type = Coding +# - code: C25208 +# label: Weight +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# +# value_quantity: # type = Quantity +# value_decimal: 45 +# unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) +# coding: # type = Coding +# - code: C28253 +# label: Milligram +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized + + creation_activity: # type = SpecimenCreationActivity. This object encapsulates data related to how a specimen was created. It is inlined because this is not a stand-alone, identified entity. + activity_type: # type = CodeableConcept. This field indicates that the activity instance here represents the initial collection from a source, rather than derivation from an existing specimen (e.g via portioning or aliquoting). + coding: # type = Coding + - code: C93435 + label: Performed Specimen Collection + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + date_ended: # type = TimePoint + offset_from_index: # type = Quantity + value_decimal: 238 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + index_time_point: # type = TimePoint + event_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because CCDH made up this 'Study Start' value to demonstrate how to specify events as a conceptual index timepoint. + - coding: # type = Coding + - code: C142714 + label: Study Start + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + + quantity_collected: # type = Quantity + value_decimal: 57 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C28253 + label: Milligram + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + + collection_site: # type = BodySite + site: # type = CodeableConcept + coding: # type = Coding + - code: C12468 + label: Lung + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Lung + label: Lung + system: http://crdc.nci.nih.gov/gdc + tag: + - original + +# execution_time_observation: # type = ExecutionTimeObservation +# - observation_type: # type = CodeableConcept +# coding: # type = Coding +# - code: time_between_excision_and_freezing # This enumerated code was generated for the harmonized model, based on the name of a direct Sample property in the GDC model (Sample.time_between_excision_and_freezing). So there is no original source code here. +# label: time between excision and freezing +# system: http://crdc.nci.nih.gov/ccdh # This is a temp local code system for terms without mappings, until we find one or get code into NCIt. +# tag: +# - harmonized +# value_quantity: # type = Quantity +# value_decimal: 15 +# unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) +# coding: # type = Coding +# - code: C48154 +# label: Minute +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized + + processing_activity: # type = SpecimenProcessingActivity. This object encapsulates data related to how a specimen was processed. It is inlined because this is not a stand-alone, identified entity. + - activity_type: # type = CodeableConcept + coding: # type = Coding + - code: C48160 + label: Freezing + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Frozen + label: Frozen + system: http://crdc.nci.nih.gov/gdc + tag: + - original + method_type: # type = CodeableConcept + coding: # type = Coding + - code: C178955 + label: Minus 80 Degrees Celsius Freezer + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: "-80" + label: "-80" + system: http://crdc.nci.nih.gov/gdc + tag: + - original + +--- + gdc_subject: + Title: GDC Subject Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713.Subject + Description: + - "This is a minimal example showing only id and identifiers. For a richer Subject record, see the examples in Demonstrator 2." + Example: # type: Subject + id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" # Local uuid assigned by this system for the Subject +# identifier: # type: Identifier +# - value: "gdc-case:18e0e996-8f23-4f53-94a5-dde38b550863" # GDC.Cases.case_id +# - value: "tcga:TCGA-13-1409" # GDC.Cases.submitter_id +# - value: "crdc:su0000001" # Proposed globally unique identifier per recommendation of the CRDC-DST + +--- + gdc_research_project: + Title: GDC ResearchProject Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713.ResearchProject + Description: + - "This is a minimal example showing only id and identifiers. For a richer Project record, see the examples in Demonstrator 2." + Example: # type = ResearchProject + id: "f2f:bc65592e-c7e2-5ab5-3c56-283ea2efc8f8" # Local uuid assigned by this system for the Research Project +# identifier: # type = Identifier +# - value: "gdc-project:TARGET-OS" # GDC.Sample.project_id +# - value: "crdc:pj1000004" # Proposed globally unique identifier per recommendation of the CRDC-DST + research_project_type: + coding: + - code: Project # Note also that because the CRDC-H collapses GDC.Program and GDC.Project into a single type called 'ResearchProject', the ResearchProject.research_project_type field is used to indicate which specific type this instance represents. + system: http://crdc.nci.nih.gov/ccdh + + + +--- +gdc_diagnosis: + Title: GDC Diagnosis Example - Sept 2021 F2F Demonstrator 1 + Schema: "ccdh.0713cc.Diagnosis" + Description: + - "CRDC-H-compliant representation of the synthetic source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "For easiest viewing, **TURN WORD WRAP OFF** so that comments don't run onto a new line." + Example: # type = Diagnosis + id: "f2f:de3468e83-4c86-4258-98d1-a986445cce73" # Local uuid assigned by this system for the Diagnosis +# identifier: # type = Identifier +# - value: "gdc-diagnosis:21a0cbbb-c778-4b2c-cd54-8a5047a3a077" # GDC.Diagnosis.diagnosis_id +# - value: "target:TARGET-40-0A4I9I-01D" # GDC.Diagnosis.submitter_id + + subject: # type = Subject + id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" + + age_at_diagnosis: # type = Quantity + value_decimal: 32518 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + + condition: # type = CodeableConcept + coding: # type = Coding + - code: C9145 + label: Osteosarcoma + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Osteosarcoma (OS) + label: Osteosarcoma (OS) + system: http://crdc.nci.nih.gov/gdc + tag: + - original +# primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C12366 +# label: Bone +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# - code: Bone +# label: Bone +# system: http://crdc.nci.nih.gov/gdc +# tag: +# - original + + stage: # type = CancerStageObservationSet + - method_type: # type = CodeableConcept + - coding: # type = Coding + - code: C125755 + label: AJCC Staging Manual 7th Edition + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: 7th + label: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + +# observations: # type = CancerStageObservation - one of many individual Stage determinations (e.g. T, N, M, Overall) about the same tumor that can comprise a single CancerStageObservationSet (here just an 'Overall' assessment, but may also include T, N, and M assessments). +# - observation_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because the staging level semantic is captured in an explicit property in the source GDC model, not a key-value pair as shown here) +# coding: # type = Coding +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# value_codeable_concept: # type = CodeableConcept +# coding: # type = Coding +# - code: C27979 +# label: Stage IVA +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# - code: Stage IVA +# label: Stage IVA +# system: http://crdc.nci.nih.gov/gdc +# tag: +# - original + + diagnosis_date: # type = TimePoint. GDC specifies date of diagnosis in two ways (the GDC.Diagnosis.year_of_diagnosis field, and GDC.Diagnosis.days_to_diagnosis field). Both are captured in a single TimePoint instance. + date_time: "2011-01-01" # Here we capture a broader indication of the year the diagnosis was made (2011). + offset_from_index: # type = Quantity + value_decimal: 579 # Here we capture the offset between an index timepoint (assumed to be the Start of Study) and the diagnosis date - which resolves to a more specific day/date. + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + index_time_point: # type = TimePoint (This nested Timepoint specifies the index time point using an event as a proxy, captured in the event_type field.) + event_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because CCDH made up this 'Study Start' value to demonstrate how to specify events as a conceptual index timepoint. + - coding: # type = Coding + - code: C142714 + label: Study Start + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + related_specimen: # type = Specimen + - id: "f2f:05f1574e-2a28-50bc-bdc1-e4c6dee92fd1" # A reference to a specimen that was used to generate this Diagnosis (the Specimen instance above). + + + diff --git a/ccdh-pilot/demonstrator-1/d1_harmonized_icdc_specimen_cc.yaml b/ccdh-pilot/demonstrator-1/d1_harmonized_icdc_specimen_cc.yaml new file mode 100644 index 0000000..6396fae --- /dev/null +++ b/ccdh-pilot/demonstrator-1/d1_harmonized_icdc_specimen_cc.yaml @@ -0,0 +1,192 @@ +icdc_specimen: + Title: ICDC Specimen Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713cc.Specimen + Description: + - "CRDC-H-compliant representation of the 'aggregate' ICDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + + Example: # type = Specimen + id: "f2f:052c671d-118a-11e9-afb9-0a9c39d33490" # Local uuid for the Specimen a assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). +# identifier: # type = Identifier (Identifier is a complex data type, but we are only showing a single field from this type) +# - value: "ncats-cop:NCATS-COP01-CCB050227 0103" # ICDC.Sample.sample_id (specified here as a CURIE, where the prefix indicates the system that assigned it) +# - value: "icdc-sample:30502" # ICDC.Sample._id (specified here as a CURIE, where the prefix indicates the system that assigned it) +# - value: "biosample:SAMEA1652206" # Proposed globally unique identifier format, per recommendation of the CRDC-DST (specified here as a CURIE, where the prefix indicates the system that assigned it) + + specimen_type: # type = CodeableConcept + coding: # type = Coding + - code: C84517 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Fresh Specimen # The preferred label of the term from NCIT. + system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Sample # The second Coding holds the original code used by the source node. Here, this is the 'type' of the entity in ICDC (Sample). + label: Sample # The human-readable label (implicitly the same as the code, which is human-readable) + system: http://crdc.nci.nih.gov/icdc # A URL for the ICDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + source_subject: # type = Subject + id: "f2f:01b2691b-63d8-11e8-bcf1-0a2705229b82" # Local uuid assigned by this system for the Subject. The Subject instance is represented separately later in this document. + source_material_type: # type = CodeableConcept (see comments on the 'specimen_type' field above for a detailed explanation of this data object's content) + coding: # type = Coding + - code: C12801 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Tissue # The preferred label of the term from NCIT. + system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Tissue # The second Coding holds the original code used by the source node. ICDC uses a readable strings for their codes. + label: Tissue # The human-readable label (implicitly the same as the code, which are human-readable in ICDC) + system: http://crdc.nci.nih.gov/icdc # A URL for the ICDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + general_tissue_pathology: # type = CodeableConcept + coding: # type = Coding + - code: C14143 + label: Malignant + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Malignant + label: Malignant + system: http://crdc.nci.nih.gov/icdc + tag: + - original + specific_tissue_pathology: # type = CodeableConcept + coding: # type = Coding + - code: C9145 + label: Osteosarcoma + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Osteosarcoma + label: Osteosarcoma + system: http://crdc.nci.nih.gov/icdc + tag: + - original + tumor_status_at_collection: # type = CodeableConcept + coding: # type = Coding + - code: C3261 + label: Metastatic Neoplasm + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Metastatic + label: Metastatic + system: http://crdc.nci.nih.gov/icdc + tag: + - original + creation_activity: # type = SpecimenCreationActivity. This object encapsulates data related to how a specimen was created. It is inlined because this is not a stand-alone, identified entity. + activity_type: # type = CodeableConcept. This field indicates that the activity instance here represents the initial collection from a source, rather than derivation from an existing specimen (e.g via portioning or aliquoting). + coding: # type = Coding + - code: C93435 + label: Performed Specimen Collection + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + date_ended: # type = TimePoint + date_time: "2010-07-23" + collection_site: # type = BodySite + site: # type = CodeableConcept + coding: # type = Coding + - code: C12468 + label: Lung + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Lung + label: Lung + system: http://crdc.nci.nih.gov/icdc + tag: + - original + processing_activity: # type = SpecimenProcessingActivity. This object encapsulates data related to how a specimen was processed. It is inlined because this is not a stand-alone, identified entity. + - activity_type: # type = CodeableConcept + coding: # type = Coding + - code: CC63521 + label: Quick Freeze + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Snap Frozen + label: Snap Frozen + system: http://crdc.nci.nih.gov/icdc + tag: + - original + +--- + icdc_subject: + Title: ICDC Subject Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713.Subject + Description: + - "This is a minimal example showing only id and identifiers. For a richer Subject record, see the examples in Demonstrator 2." + Example: # type: Subject + id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" # Local uuid assigned by this system for the Subject +# identifier: # type: Identifier +# - value: "icdc-case:30196" # ICDC.Cases.case_id +# - value: "crdc:su0000003" # Proposed globally unique identifier per recommendation of the CRDC-DST + +--- +icdc_diagnosis: + Title: ICDC Diagnosis Example - Sept 2021 F2F Demonstrator 1 + Schema: "ccdh.0713cc.Diagnosis" + Description: + - "CRDC-H-compliant representation of the synthetic source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "For easiest viewing, **TURN WORD WRAP OFF** so that comments don't run onto a new line." + Example: # type = Diagnosis + id: "f2f:de3468e83-4c86-4258-98d1-a986445cce73" # Local uuid assigned by this system for the Diagnosis +# identifier: # type = Identifier +# - value: "icdc-diagnosis:30279" # ICDC.Diagnosis._id + subject: # type = Subject + id: "f2f:01b2691b-63d8-11e8-bcf1-0a2705229b82" + condition: # type = CodeableConcept + coding: # type = Coding + - code: C9145 + label: Osteosarcoma + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Osteosarcoma (OS) + label: Osteosarcoma (OS) + system: http://crdc.nci.nih.gov/icdc + tag: + - original +# primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C12366 +# label: Bone +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# - code: Bone +# label: Bone +# system: http://crdc.nci.nih.gov/icdc +# tag: +# - original +# stage: # type = CancerStageObservationSet +# - observations: # type = CancerStageObservation - one of many individual Stage determinations (e.g. T, N, M, Overall) about the same tumor that can comprise a single CancerStageObservationSet (here just an 'Overall' assessment, but may also include T, N, and M assessments). +# - observation_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because the staging level semantic is captured in an explicit property in the source PDC model, not a key-value pair as shown here) +# coding: # type = Coding +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# value_codeable_concept: # type = CodeableConcept +# coding: # type = Coding +# - code: C27971 +# label: Stage IV +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# - code: IV +# label: IV +# system: http://crdc.nci.nih.gov/icdc +# tag: +# - original + diagnosis_date: # type = TimePoint + date_time: "2013-06-14" + related_specimen: # type = Specimen + - id: "f2f:052c671d-118a-11e9-afb9-0a9c39d33490" # A reference to a specimen that was used to generate this Diagnosis (the Specimen instance above). + + + diff --git a/ccdh-pilot/demonstrator-1/d1_harmonized_pdc_specimen_cc.yaml b/ccdh-pilot/demonstrator-1/d1_harmonized_pdc_specimen_cc.yaml new file mode 100644 index 0000000..93f39dd --- /dev/null +++ b/ccdh-pilot/demonstrator-1/d1_harmonized_pdc_specimen_cc.yaml @@ -0,0 +1,341 @@ +--- +pdc_specimen: + Title: PDC Specimen Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713cc.Specimen + Description: + - "CRDC-H-compliant representation of the 'aggregate' PDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + + Example: # type = Specimen + id: "f2f:ecc2bf49-204d-11e9-b7f8-0a80fada099c" # Local uuid for the Specimen a assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). +# identifier: # type = Identifier (Identifier is a complex data type, but we are only showing a single field from this type) +# - value: "tcga-coad:C3N-01648-08" # PDC.Sample.sample_submitter_id (specified here as a CURIE, where the prefix indicates the system that assigned it) +# - value: "pdc-sample:ecc2bf49-204d-11e9-b7f8-0a80fada099c" # PDC.Sample.sample_id (specified here as a CURIE, where the prefix indicates the system that assigned it) +# - value: "biosample:SAMEA1476035" # Proposed globally unique identifier format, per recommendation of the CRDC-DST (specified here as a CURIE, where the prefix indicates the system that assigned it) + + specimen_type: # type = CodeableConcept + coding: # type = Coding + - code: C84517 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Fresh Specimen # The preferred label of the term from NCIT. + system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Sample # The second Coding holds the original code used by the source node. Here, this is the 'type' of the entity in PDC (which defines separate entities for differet types of Specimens - Sample, Portion, Aliquit, Analyte). + label: Sample # The human-readable label (implicitly the same as the code which are human-readable in PDC) + system: http://crdc.nci.nih.gov/pdc # A URL for the PDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + associated_project: # type = ResearchProject. + id: "f2f:69886602-a4f1-4ad4-ba56-a0e031c2e294" # Local uuid assigned by this system for the Research Project. The Project instance is represented separately later in this document. We will define a formal way to specify references in the next phase of work. + research_project_type: # type = CodeableConcept + coding: # type = Coding + - code: C47885 # Note also that because the CRDC-H collapses PDC.Program and PDC.Project into a single type called 'ResearchProject', the ResearchProject.research_project_type field is used to indicate which specific type this instance represents. + label: Project + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + source_subject: # type = Subject + id: "f2f:55bad781-96ce-537c-ab5c-7492c31c836c" # Local uuid assigned by this system for the Subject. The Subject instance is represented separately later in this document. + source_material_type: # type = CodeableConcept (see comments on the 'specimen_type' field above for a detailed explanation of this data object's content) + coding: # type = Coding + - code: C18009 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Tumor Tissue # The preferred label of the term from NCIT. + system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Tumor # The second Coding holds the original code used by the source node. PDC uses a readable strings for their codes. + label: Tumor # The human-readable label (implicitly the same as the code, which are human-readable in PDC) + system: http://crdc.nci.nih.gov/pdc # A URL for the PDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + general_tissue_pathology: # type = CodeableConcept + coding: # type = Coding + - code: C18009 + label: Tumor Tissue + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Tumor + label: Tumor + system: http://crdc.nci.nih.gov/pdc + tag: + - original + specific_tissue_pathology: # type = CodeableConcept + coding: # type = Coding + - code: C9145 + label: Osteosarcoma + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Osteosarcoma (OS) + label: Osteosarcoma (OS) + system: http://crdc.nci.nih.gov/pdc + tag: + - original + tumor_status_at_collection: # type = CodeableConcept + coding: # type = Coding + - code: C3261 + label: Metastatic Neoplasm + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Metastatic + label: Metastatic + system: http://crdc.nci.nih.gov/pdc + tag: + - original +# quantity_measure: # type = QuantityMeasureObservation +# - observation_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because the weight of a specimen is captured in PDC using a dedicated property (Sample.current_weight), not as a key-vaule pair as we do here) +# coding: # type = Coding +# - code: C25208 +# label: Weight +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# value_quantity: # type = Quantity +# value_decimal: 224 +# unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) +# coding: # type = Coding +# - code: C28253 +# label: Milligram +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized + creation_activity: # type = SpecimenCreationActivity. This object encapsulates data related to how a specimen was created. It is inlined because this is not a stand-alone, identified entity. + activity_type: # type = CodeableConcept. This field indicates that the activity instance here represents the initial collection from a source, rather than derivation from an existing specimen (e.g via portioning or aliquoting). + coding: # type = Coding + - code: C93435 + label: Performed Specimen Collection + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + date_ended: # type = TimePoint + offset_from_index: # type = Quantity + value_decimal: 121 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + index_time_point: # type = TimePoint + event_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because CCDH made up this 'Study Start' value to demonstrate how to specify events as a conceptual index timepoint. + - coding: # type = Coding + - code: C142714 + label: Study Start + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + + quantity_collected: # type = Quantity + value_decimal: 224 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C28253 + label: Milligram + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + + collection_site: # type = BodySite + site: # type = CodeableConcept + coding: # type = Coding + - code: C12468 + label: Lung + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Lung + label: Lung + system: http://crdc.nci.nih.gov/pdc + tag: + - original + +# execution_time_observation: # type = ExecutionTimeObservation +# - observation_type: # type = CodeableConcept +# coding: # type = Coding +# - code: time_between_excision_and_freezing # This enumerated code was generated for the harmonized model, based on the name of a direct Sample property in the PDC model (Sample.time_between_excision_and_freezing). So there is no original source code here. +# label: time between excision and freezing +# system: http://crdc.nci.nih.gov/ccdh # This is a temp local code system for terms without mappings, until we find one or get code into NCIt. +# tag: +# - harmonized +# value_quantity: # type = Quantity +# value_decimal: 20 +# unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) +# coding: # type = Coding +# - code: C48154 +# label: Minute +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized + + processing_activity: # type = SpecimenProcessingActivity. This object encapsulates data related to how a specimen was processed. It is inlined because this is not a stand-alone, identified entity. + - activity_type: # type = CodeableConcept + coding: # type = Coding + - code: CC63521 + label: Quick Freeze + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Snap Frozen + label: Snap Frozen + system: http://crdc.nci.nih.gov/pdc + tag: + - original + method_type: # type = CodeableConcept + coding: # type = Coding + - code: C178951 + label: Liquid Nitrogen Freezer + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: LN2 + label: LN2 + system: http://crdc.nci.nih.gov/pdc + tag: + - original + +--- + pdc_subject: + Title: PDC Subject Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713.Subject + Description: + - "This is a minimal example showing only id and identifiers. For a richer Subject record, see the examples in Demonstrator 2." + Example: # type: Subject + id: "f2f:55bad781-96ce-537c-ab5c-7492c31c836c" # Local uuid assigned by this system for the Subject +# identifier: # type: Identifier +# - value: "pdc-case:3073d082-63d8-11e8-bcf1-0a2705229b82" # PDC.Cases.case_id +# - value: "tcga-coad:TCGA-AA-3518" # PDC.Cases.submitter_id +# - value: "crdc:su0000002" # Proposed globally unique identifier per recommendation of the CRDC-DST + +--- + pdc_research_project: + Title: PDC ResearchProject Example - Sept 2021 F2F Demonstrator 1 + Schema: ccdh.0713.ResearchProject + Description: + - "This is a minimal example showing only id and identifiers. For a richer Project record, see the examples in Demonstrator 2." + Example: # type = ResearchProject + id: "f2f:69886602-a4f1-4ad4-ba56-a0e031c2e294" # Local uuid assigned by this system for the Research Project +# identifier: # type = Identifier +# - value: "pdc-project:TCGA-COAD" # PDC.Sample.project_id +# - value: "crdc:pj1000005" # Proposed globally unique identifier per recommendation of the CRDC-DST + research_project_type: # type = CodeableConcept + coding: # type = Coding + - code: C47885 # Note also that because the CRDC-H collapses PDC.Program and PDC.Project into a single type called 'ResearchProject', the ResearchProject.research_project_type field is used to indicate which specific type this instance represents. + label: Project + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +--- +pdc_diagnosis: + Title: PDC Diagnosis Example - Sept 2021 F2F Demonstrator 1 + Schema: "ccdh.0713cc.Diagnosis" + Description: + - "CRDC-H-compliant representation of the synthetic source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "For easiest viewing, **TURN WORD WRAP OFF** so that comments don't run onto a new line." + Example: # type = Diagnosis + id: "f2f:62199412-6428-11e8-bcf1-0a2705229b82" # Local uuid assigned by this system for the Diagnosis +# identifier: # type = Identifier +# - value: "pdc-diagnosis:e3dd3c20-1fcb-11e9-b7f8-0a80fada099c" # PDC.Diagnosis.diagnosis_id +# - value: "TCGA-COAD:C3N-01648-DIAG" # PDC.Diagnosis.submitter_id + + subject: # type = Subject + id: "f2f:55bad781-96ce-537c-ab5c-7492c31c836c" + + age_at_diagnosis: # type = Quantity + value_decimal: 20144 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + + condition: # type = CodeableConcept + coding: # type = Coding + - code: C9145 + label: Osteosarcoma + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: Osteosarcoma (OS) + label: Osteosarcoma (OS) + system: http://crdc.nci.nih.gov/pdc + tag: + - original +# primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C173840 +# label: Maxillofacial Bone +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# - code: Bones of skull and face and associated joints +# label: Bones of skull and face and associated joints +# system: http://crdc.nci.nih.gov/pdc +# tag: +# - original + + stage: # type = CancerStageObservationSet + - method_type: # type = CodeableConcept + - coding: # type = Coding + - code: C146985 + label: AJCC Staging Manual 8th Edition + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + - code: 8th + label: 8th + system: http://crdc.nci.nih.gov/pdc + tag: + - original + +# observations: # type = CancerStageObservation - one of many individual Stage determinations (e.g. T, N, M, Overall) about the same tumor that can comprise a single CancerStageObservationSet (here just an 'Overall' assessment, but may also include T, N, and M assessments). +# - observation_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because the staging level semantic is captured in an explicit property in the source PDC model, not a key-value pair as shown here) +# coding: # type = Coding +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# value_codeable_concept: # type = CodeableConcept +# coding: # type = Coding +# - code: C27971 +# label: Stage IV +# system: http://ncithesaurus.nci.nih.gov +# tag: +# - harmonized +# - code: Stage IV +# label: Stage IV +# system: http://crdc.nci.nih.gov/pdc +# tag: +# - original + + diagnosis_date: # type = TimePoint. PDC specifies date of diagnosis in two ways (the PDC.Diagnosis.year_of_diagnosis field, and PDC.Diagnosis.days_to_diagnosis field). Both are captured in a single TimePoint instance. + date_time: "2009-01-01" # Here we capture a broader indication of the year the diagnosis was made (2011). + offset_from_index: # type = Quantity + value_decimal: 0 # Here we capture the offset between an index timepoint (assumed to be the Start of Study) and the diagnosis date - which resolves to a more specific day/date. We used the value '0' because this is the only value in the PDC data for this field. + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + index_time_point: # type = TimePoint (This nested Timepoint specifies the index time point using an event as a proxy, captured in the event_type field.) + event_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because CCDH made up this 'Study Start' value to demonstrate how to specify events as a conceptual index timepoint. + - coding: # type = Coding + - code: C142714 + label: Study Start + system: http://ncithesaurus.nci.nih.gov + tag: + - harmonized + related_specimen: # type = Specimen + - id: "f2f:ecc2bf49-204d-11e9-b7f8-0a80fada099c" # A reference to a specimen that was used to generate this Diagnosis (the Specimen instance above). + + + diff --git a/ccdh-pilot/demonstrator-2/README.md b/ccdh-pilot/demonstrator-2/README.md new file mode 100644 index 0000000..32dc18d --- /dev/null +++ b/ccdh-pilot/demonstrator-2/README.md @@ -0,0 +1,2 @@ +Files in this directory were copied here from +https://github.com/cancerDHC/data-model-harmonization/tree/d83c2853ea6cdd8dfbb9204c2cd4c335969660c6/data-examples/f2f-2021-09-data-examples diff --git a/ccdh-pilot/demonstrator-2/d2_gdc_TCGA-13-1409_cc.yaml b/ccdh-pilot/demonstrator-2/d2_gdc_TCGA-13-1409_cc.yaml new file mode 100644 index 0000000..f0013e9 --- /dev/null +++ b/ccdh-pilot/demonstrator-2/d2_gdc_TCGA-13-1409_cc.yaml @@ -0,0 +1,223 @@ +--- +gdc_subject: + Title: GDC Subject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.Subject + Description: + - "CRDCH-compliant representation of the GDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + Example: # type = Subject + id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" # Local uuid for the Subject as assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). +# identifier: # type = Identifier +# - value: "gdc-case:18e0e996-8f23-4f53-94a5-dde38b550863" # GDC.Cases.case_id +# - value: "tcga:TCGA-13-1409" # GDC.Cases.submitter_id +# - value: "crdc:su0000005" # Proposed globally unique identifier per recommendation of the CRDC-DST + ethnicity: # type = CodeableConcept + coding: # type = Coding + - code: C41222 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Not Hispanic or Latino # The preferred label of the term from NCIT. + system: https://ncithesaurus.nci.nih.gov/ # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: not hispanic or latino # The second Coding holds the original code used by the source node. + label: not hispanic or latino # The human-readable label (implicitly the same as the code, which are human-readable in GDC) + system: http://crdc.nci.nih.gov/gdc # A URL for the GDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + race: # type = CodeableConcept + - coding: # type = Coding + - code: C41261 + label: White + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: white + label: white + system: http://crdc.nci.nih.gov/gdc + tag: + - original + sex: # type = CodeableConcept + coding: # type = Coding + - code: C16576 + label: Female + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: female + label: female + system: http://crdc.nci.nih.gov/gdc + tag: + - original + vital_status: # type = CodeableConcept + coding: # type = Coding + - code: C28554 + label: Dead + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Dead + label: Dead + system: http://crdc.nci.nih.gov/gdc + tag: + - original + species: # type = CodeableConcept + coding: # type = Coding + - code: C14225 + label: Human + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + year_of_birth: 1935 + age_at_death: # type = Quantity + value_decimal: 28578 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + +--- +gdc_diagnosis: + Title: GDC Diagnosis Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.Diagnosis + Example: # type = Diagnosis + id: "f2f:fe908e53-4b99-4150-94d2-b086575cde41" +# identifier: # type = Identifier +# - value: "gdc-diagnosis:6b0f33e6-884d-5a93-8335-9f55569790a7" # GDC.Diagnosis.diagnosis_id + morphology: # type = CodeableConcept + coding: # type = Coding + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: 8441/3 + label: Serous cystadenocarcinoma, NOS + system: http://who.int/icdo3/ + tag: + - original +# primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C12404 +# label: Ovary +# system: https://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Ovary +# label: Ovary +# system: http://crdc.nci.nih.gov/gdc +# tag: +# - original + stage: # type = CancerStageObservationSet + - method_type: # type = CodeableConcept + - coding: # type = Coding + - code: C125738 + label: FIGO Stage + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +# - observations: # type = CancerStageObservation +# - observation_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# value_codeable_concept: # type = CodeableConcept +# coding: # type = Coding +# - code: C96258 +# label: FIGO Stage IIIC +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Stage IIIC +# label: Stage IIIC +# system: http://crdc.nci.nih.gov/gdc +# tag: +# - original + condition: # type = CodeableConcept + coding: # type = Coding + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Serous cystadenocarcinoma, NOS # GDC.Diagnosis.primary_diagnosis + label: Serous cystadenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C56.9 # GDC.Diagnosis.icd_10_code + label: Malignant neoplasm of unspecified ovary # This is the ICD-10 preferred term for C56.9 + system: http://who.int/icd10/ + tag: + - original + diagnosis_date: + date_time: "2008-01-01" + age_at_diagnosis: # type = Quantity + value_decimal: 26836 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + subject: # type = Subject + id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" + +--- +gdc_research_project: + Title: GDC ResearchProject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.ResearchProject + Example: # type = ResearchProject + id: "f2f:ff364424-8506-41c4-b5e0-410339462560" # Local uuid assigned by this system for the ResearchProject +# identifier: # type = Identifier +# - value: "gdc-project:TCGA-OV" # GDC.Project.project_id +# - value: "crdc:pj1000015" # Proposed globally unique identifier per recommendation of the CRDC-DST + name: Ovarian Serous Cystadenocarcinoma + research_project_type: # type = CodeableConcept + coding: # type = Coding + - code: C47885 + label: Project + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +# part_of: # type = ResearchProject +# - id: "f2f:6b0cc2d2-2fec-4049-8ac4-77edb6d914f8" # Local uuid assigned by this system for the Research Project +# identifier: # type = Identifier +# - value: "gdc-program:b80aa962-9650-5110-b3eb-bd087da808db" +# - value: "dbgap:phs000178" # GDC.Project.dbgap_accession_number +# - value: "crdc:pg1000013" # Proposed globally unique identifier per recommendation of the CRDC-DST +# research_project_type: # type = CodeableConcept +# coding: # type = Coding +# - code: "C52647" +# label: Program +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# name: TCGA + +--- +gdc_research_subject: + Title: GDC ResearchSubject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.ResearchSubject + Example: # type = ResearchSubject + id: "f2f:bceb9b07-40bc-4d3e-a65a-6f3cc7e44827" + # Below is an association by reference only +# associated_subject: # type = Subject +# id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" + # Below is an association by inline inclusion +# member_of_research_project: # type = ResearchProject +# id: "f2f:ff364424-8506-41c4-b5e0-410339462560" +# research_project_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C47885 +# label: Project +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized diff --git a/ccdh-pilot/demonstrator-2/d2_harmonized_TCGA-13-1409_cc.yaml b/ccdh-pilot/demonstrator-2/d2_harmonized_TCGA-13-1409_cc.yaml new file mode 100644 index 0000000..c56ab39 --- /dev/null +++ b/ccdh-pilot/demonstrator-2/d2_harmonized_TCGA-13-1409_cc.yaml @@ -0,0 +1,283 @@ +--- +harmonized_subject: + Title: Harmonized Subject Example + Schema: ccdh.0713cc.Subject + Description: + - "CRDCH-compliant representation of an aggregated and harmonized data example from multiple needs. Source data described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + Example: # type = Subject + id: "f2f:9731ddf7-5524-4e12-beb9-adfc044ea0a6" +# identifier: # type = Identifier +# - value: "pdc-case:3a36a497-63d7-11e8-bcf1-0a2705229b82" # PDC.Cases.case_id +# - value: "tcga:TCGA-13-1409" # PDC.Cases.case_submitter_id +# - value: "gdc-case:18e0e996-8f23-4f53-94a5-dde38b550863" # GDC.Cases.case_id +# - value: "tcga:TCGA-13-1409" # GDC.Cases.submitter_id +# - value: "idc-case:ffde0494-7583-44ca-9e9d-902e84a3b4b3" # IDC.dicom_all.case_id +# - value: "tcga:TCGA-13-1409" # IDC.dicom_all.submitter_id +# - value: "crdc:su0000005" # Proposed globally unique identifier per recommendation of the CRDC-DST + ethnicity: + coding: + - code: C41222 + label: Not Hispanic or Latino + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: not hispanic or latino + label: not hispanic or latino + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: Not Hispanic or Latino + label: Not Hispanic or Latino + system: http://crdc.nci.nih.gov/pdc + tag: + - original + race: + - coding: + - code: C41261 + label: White + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: white + label: white + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: White + label: White + system: http://crdc.nci.nih.gov/pdc + tag: + - original + sex: + coding: + - code: C16576 + label: Female + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: female + label: female + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: Female + label: Female + system: http://crdc.nci.nih.gov/pdc + tag: + - original + - code: F + label: F + system: http://crdc.nci.nih.gov/idc + tag: + - original + vital_status: + coding: + - code: C28554 + label: Dead + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Dead + label: Dead + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: Dead + label: Dead + system: http://crdc.nci.nih.gov/pdc + tag: + - original + year_of_birth: 1935 + species: + coding: + - code: C14225 + label: Human + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Human + label: Human + system: http://crdc.nci.nih.gov/idc + tag: + - original + age_at_death: # type = Quantity + value_decimal: 28578 + unit: + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + +--- +harmonized_diagnosis: + Title: Harmonized Diagnosis Example + Schema: ccdh.0713cc.Diagnosis + Example: # type = Diagnosis + id: "f2f:e5a619d3-40b4-4aaa-a40e-c2a0d75e8d79" +# identifier: # type = Identifier +# - value: "pdc-diagnosis:ff2f0efb-70ca-11e8-bcf1-0a2705229b82" # PDC.Diagnosis.diagnosis_id +# - value: "tcga:TCGA-13-1409-DX" # PDC.Diagnosis.diagnosis_submitter_id +# - value: "gdc-diagnosis:6b0f33e6-884d-5a93-8335-9f55569790a7" # GDC.Diagnosis.diagnosis_id +# - value: "tcga:TCGA-13-1409_diagnosis" # GDC.Diagnosis.submitter_id + subject: # type = Subject + id: "f2f:9731ddf7-5524-4e12-beb9-adfc044ea0a6" + age_at_diagnosis: # type = Quantity + value_decimal: 26836 + unit: + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + diagnosis_date: + date_time: "2008-01-01" + condition: + coding: + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Serous cystadenocarcinoma, NOS # GDC.Diagnosis.primary_diagnosis + label: Serous cystadenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: Serous cystadenocarcinoma, NOS # GDC.Diagnosis.primary_diagnosis + label: Serous cystadenocarcinoma, NOS + system: http://crdc.nci.nih.gov/pdc + tag: + - original + - code: C56.9 # GDC.Diagnosis.icd_10_code + label: Malignant neoplasm of unspecified ovary # This is the ICD-10 preferred term for C56.9 + system: http://who.int/icd10/ + tag: + - original + morphology: + coding: + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: 8441/3 + label: Serous cystadenocarcinoma, NOS + system: http://who.int/icdo3/ + tag: + - original + - code: 8441/3 + label: Serous cystadenocarcinoma, NOS + system: http://who.int/icdo3/ + tag: + - original +# primary_site: +# - site: +# coding: +# - code: C12404 +# label: Ovary +# system: https://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Ovary +# label: Ovary +# system: http://crdc.nci.nih.gov/gdc +# tag: +# - original +# - code: Ovary +# label: Ovary +# system: http://crdc.nci.nih.gov/pdc +# tag: +# - original +# - code: Ovary +# label: Ovary +# system: http://crdc.nci.nih.gov/idc +# tag: +# - original + stage: + - method_type: + - coding: + - code: C125738 + label: FIGO Stage + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +# - observations: +# - observation_type: +# coding: +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# value_codeable_concept: +# coding: +# - code: C96258 +# label: FIGO Stage IIIC +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Stage IIIC +# label: Stage IIIC +# system: http://crdc.nci.nih.gov/gdc +# tag: +# - original +# - code: Stage IIIC +# label: Stage IIIC +# system: http://crdc.nci.nih.gov/pdc +# tag: +# - original + +--- +harmonized_research_project: + Title: PDC ResearchProject Example + Schema: ccdh.0713cc.ResearchProject + Example: # type = ResearchProject + id: "f2f:77ed81c1-5e63-481e-889d-604844807a10" +# identifier: # type = Identifier +# - value: "crdc:pj1000015" # Proposed globally unique identifier per recommendation of the CRDC-DST +# - value: "gdc-project:TCGA-OV" # GDC.Project.project_id +# - value: "idc-project:tcga_ov" # IDC.dicom_all.collection_id + research_project_type: + coding: + - code: C47885 + label: Project + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + name: Ovarian Serous Cystadenocarcinoma +# part_of: +# - research_project_type: +# coding: +# - code: C52647 +# label: Program +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# id: "f2f:c19a8e03-f674-4124-b8ac-2222e08de978" +# identifier: +# - value: "crdc:pg1000013" # Proposed globally unique identifier per recommendation of the CRDC-DST +# - value: "dbgap:phs000178" # GDC.Project.dbgap_accession_number +# name: TCGA + +--- +harmonized_research_subject: + Title: Harmonized ResearchSubject Example + Schema: ccdh.0713cc.ResearchSubject + Example: # type = ResearchSubject + id: "f2f:2b66c18b-dec1-4a7d-bbf5-8c435fd85efc" +# associated_subject: # type = Subject +# id: "f2f:9731ddf7-5524-4e12-beb9-adfc044ea0a6" +# member_of_research_project: # type = ResearchProject +# research_project_type: +# coding: +# - code: C47885 +# label: Project +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# id: "f2f:77ed81c1-5e63-481e-889d-604844807a10" diff --git a/ccdh-pilot/demonstrator-2/d2_idc_TCGA-13-1409_cc.yaml b/ccdh-pilot/demonstrator-2/d2_idc_TCGA-13-1409_cc.yaml new file mode 100644 index 0000000..9539541 --- /dev/null +++ b/ccdh-pilot/demonstrator-2/d2_idc_TCGA-13-1409_cc.yaml @@ -0,0 +1,97 @@ +--- +idc_subject: + Title: IDC Subject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.Subject + Description: + - "CRDCH-compliant representation of the IDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + Example: # type = Subject + id: "f2f:4e9c2068-6b9c-4944-9a62-ab38f408d777" # Local uuid for the Subject as assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). +# identifier: # type = Identifier +# - value: "idc-case:ffde0494-7583-44ca-9e9d-902e84a3b4b3" # IDC.dicom_all.case_id +# - value: "tcga:TCGA-13-1409" # IDC.dicom_all.submitter_id +# - value: "crdc:su0000025" # Proposed globally unique identifier per recommendation of the CRDC-DST + sex: # type = CodeableConcept + coding: # type = Coding + - code: C16576 + label: Female + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: F + label: F + system: http://crdc.nci.nih.gov/idc + tag: + - original + species: # type = CodeableConcept + coding: # type = Coding + - code: C14225 + label: Human + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Human + label: Human + system: http://crdc.nci.nih.gov/idc + tag: + - original + +--- +idc_diagnosis: + Title: IDC Diagnosis Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.Diagnosis + Example: # type = Diagnosis + id: "f2f:b2dcfb3a-8a28-4325-9202-7ca70bf24fd6" +# primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C12404 +# label: Ovary +# system: https://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Ovary +# label: Ovary +# system: http://crdc.nci.nih.gov/idc +# tag: +# - original + subject: # type = Subject + id: "f2f:4e9c2068-6b9c-4944-9a62-ab38f408d777" + +--- +idc_research_project: + Title: IDC ResearchProject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.ResearchProject + Example: # type = ResearchProject + id: "f2f:3a24f021-7fb9-478f-81bc-e114e7263960" # Local uuid assigned by this system for the ResearchProject +# identifier: # type = Identifier +# - value: "idc-project:tcga_ov" # IDC.dicom_all.collection_id +# - value: "crdc:pj1000015" # Proposed globally unique identifier per recommendation of the CRDC-DST + research_project_type: # type = CodeableConcept + coding: # type = Coding + - code: C47885 + label: Project + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + +--- +idc_research_subject: + Title: IDC ResearchSubject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.ResearchSubject + Example: # type = ResearchSubject + id: "f2f:15b7b028-4b37-4642-938b-5fd58d3d4f75" + # Below is an association by reference only +# associated_subject: # type = Subject +# id: "f2f:4e9c2068-6b9c-4944-9a62-ab38f408d777" +# # Below is an association by inline inclusion +# member_of_research_project: # type = ResearchProject +# id: "f2f:3a24f021-7fb9-478f-81bc-e114e7263960" +# research_project_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C47885 +# label: Project +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized diff --git a/ccdh-pilot/demonstrator-2/d2_pdc_TCGA-13-1409_cc.yaml b/ccdh-pilot/demonstrator-2/d2_pdc_TCGA-13-1409_cc.yaml new file mode 100644 index 0000000..4029356 --- /dev/null +++ b/ccdh-pilot/demonstrator-2/d2_pdc_TCGA-13-1409_cc.yaml @@ -0,0 +1,219 @@ +--- +pdc_subject: + Title: PDC Subject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.Subject + Description: + - "CRDCH-compliant representation of the PDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" + - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" + - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." + Example: # type = Subject + id: "f2f:c59cec71-88b1-439e-b7c5-b2498eaaca3a" # Local uuid for the Subject as assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). +# identifier: # type = Identifier +# - value: "pdc-case:3a36a497-63d7-11e8-bcf1-0a2705229b82" # PDC.Cases.case_id +# - value: "tcga:TCGA-13-1409" # PDC.Cases.case_submitter_id +# - value: "crdc:su0000005" # Proposed globally unique identifier per recommendation of the CRDC-DST + ethnicity: # type = CodeableConcept + coding: # type = Coding + - code: C41222 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. + label: Not Hispanic or Latino # The preferred label of the term from NCIT. + system: https://ncithesaurus.nci.nih.gov/ # A URL for the NCIT system (this is likely not the url we would ultimately use) + tag: # A tag indicating this to be the harmonized code for this concept + - harmonized + - code: Not Hispanic or Latino # The second Coding holds the original code used by the source node. + label: Not Hispanic or Latino # The human-readable label (implicitly the same as the code, which are human-readable in GDC) + system: http://crdc.nci.nih.gov/pdc # A URL for the PDC system (we made this up - t.b.d. what an official URL would look like) + tag: # A 'tag' indicating this to be the code for this concept in the original source data. + - original + race: # type = CodeableConcept + - coding: # type = Coding + - code: C41261 + label: White + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: White + label: White + system: http://crdc.nci.nih.gov/pdc + tag: + - original + sex: # type = CodeableConcept + coding: # type = Coding + - code: C16576 + label: Female + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Female + label: Female + system: http://crdc.nci.nih.gov/pdc + tag: + - original + vital_status: # type = CodeableConcept + coding: # type = Coding + - code: C28554 + label: Dead + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Dead + label: Dead + system: http://crdc.nci.nih.gov/pdc + tag: + - original + year_of_birth: 1935 + species: # type = CodeableConcept + coding: # type = Coding + - code: C14225 + label: Human + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + age_at_death: # type = Quantity + value_decimal: 28578 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + +--- +pdc_diagnosis: + Title: PDC Diagnosis Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.Diagnosis + Example: # type = Diagnosis + id: "f2f:424098d8-242f-4d8b-9ea7-6f73b4b2ec4c" +# identifier: # type = Identifier +# - value: "pdc-diagnosis:ff2f0efb-70ca-11e8-bcf1-0a2705229b82" # PDC.Diagnosis.diagnosis_id +# - value: "tcga:TCGA-13-1409-DX" # PDC.Diagnosis.diagnosis_submitter_id + subject: # type = Subject + id: "f2f:c59cec71-88b1-439e-b7c5-b2498eaaca3a" + age_at_diagnosis: # type = Quantity + value_decimal: 26836 + unit: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because unit of measure is not explicitly declared in the source data - so there is no original value.) + coding: # type = Coding + - code: C25301 + label: Day + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + # unit: days + # year_at_diagnosis: 2008 + diagnosis_date: + date_time: "2008-01-01" + condition: # type = CodeableConcept + coding: # type = Coding + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: Serous cystadenocarcinoma, NOS # GDC.Diagnosis.primary_diagnosis + label: Serous cystadenocarcinoma, NOS + system: http://crdc.nci.nih.gov/pdc + tag: + - original + morphology: # type = CodeableConcept + coding: # type = Coding + - code: C3778 + label: Serous Cystadenocarcinoma + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + - code: 8441/3 + label: Serous cystadenocarcinoma, NOS + system: http://who.int/icdo3/ + tag: + - original +# primary_site: # type = BodySite +# - site: # type = CodeableConcept +# coding: # type = Coding +# - code: C12404 +# label: Ovary +# system: https://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Ovary +# label: Ovary +# system: http://crdc.nci.nih.gov/pdc +# tag: +# - original + stage: # type = CancerStageObservationSet + - method_type: # type = CodeableConcept + - coding: # type = Coding + - code: C125738 + label: FIGO Stage + system: https://ncithesaurus.nci.nih.gov/ + tag: + - harmonized +# - observations: # type = CancerStageObservation +# - observation_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C25605 +# label: Overall +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# value_codeable_concept: # type = CodeableConcept +# coding: # type = Coding +# - code: C96258 +# label: FIGO Stage IIIC +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# - code: Stage IIIC +# label: Stage IIIC +# system: http://crdc.nci.nih.gov/pdc +# tag: +# - original + +--- +pdc_research_project: + Title: PDC ResearchProject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.ResearchProject + Example: # type = ResearchProject + id: "f2f:7196cb06-6999-4e6e-9b78-e1b4233629ab" +# identifier: # type = Identifier +# - value: "pdc-project:CPTAC-TCGA" +# - value: "crdc:pj1000017" # Proposed globally unique identifier per recommendation of the CRDC-DST + research_project_type: # type = CodeableConcept + coding: # type = Coding + - code: C47885 + label: Project + system: http://ncithesaurus.nci.nih.gov/ + tag: + - harmonized + name: CPTAC2 Retrospective +# part_of: +# - research_project_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C52647 +# label: Program +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# id: "f2f:c19a8e03-f674-4124-b8ac-2222e08de978" +# identifier: +# - value: "pdc-program:10251935-5540-11e8-b664-00a098d917f8" +# - value: "pdc-program:Clinical Proteomic Tumor Analysis Consortium" +# - value: "crdc:pg1000023" # Proposed globally unique identifier per recommendation of the CRDC-DST +# name: Clinical Proteomic Tumor Analysis Consortium + +--- +pdc_research_subject: + Title: PDC ResearchSubject Example - Sept 2021 F2F Demonstrator 2 + Schema: ccdh.0713cc.ResearchSubject + Example: # type = ResearchSubject + id: "f2f:1306ef67-11cd-4e72-a4db-ae05584460a1" +# associated_subject: # type = Subject +# id: "f2f:c59cec71-88b1-439e-b7c5-b2498eaaca3a" +# member_of_research_project: # type = ResearchProject +# research_project_type: # type = CodeableConcept +# coding: # type = Coding +# - code: C47885 +# label: Project +# system: http://ncithesaurus.nci.nih.gov/ +# tag: +# - harmonized +# id: "f2f:7196cb06-6999-4e6e-9b78-e1b4233629ab" diff --git a/ccdh-pilot/imported-node-data/gdc-head-and-mouth.yaml b/ccdh-pilot/imported-node-data/gdc-head-and-mouth.yaml new file mode 100644 index 0000000..92ece17 --- /dev/null +++ b/ccdh-pilot/imported-node-data/gdc-head-and-mouth.yaml @@ -0,0 +1,45365 @@ +gdc_head_and_mouth_case_0_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_0_diagnosis_0 + identifier: + - value: 5d2d67d1-4611-4a18-9a66-89823aaa8e3c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_0 + identifier: + - value: cd7e514f-71ba-4cc1-b74a-a22c6248169c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD6426 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19592 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Adenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8140/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_0_sample_0 + identifier: + - value: bdc73f48-dc0b-487d-abbe-e3a977b6830a + system: http://crdc.nci.nih.gov/gdc + - value: AD6426_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_0_sample_0_subject + identifier: + - value: AD6426_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cd7e514f-71ba-4cc1-b74a-a22c6248169c + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_1_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_1_diagnosis_0 + identifier: + - value: 706b1290-3a85-54ea-a123-e8bd14b085bc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_1 + identifier: + - value: 9023c9bf-02a0-4396-8161-304089957b62 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6012 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24286 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_1_sample_0 + identifier: + - value: 8b2588c8-4261-492b-b173-2490a5de668f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6012-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_1_sample_0_subject + identifier: + - value: TCGA-CN-6012-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9023c9bf-02a0-4396-8161-304089957b62 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_1_sample_1 + identifier: + - value: badeaed0-2625-4a4d-bb95-d295e2c32c01 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6012-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_1_sample_1_subject + identifier: + - value: TCGA-CN-6012-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9023c9bf-02a0-4396-8161-304089957b62 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_1_sample_2 + identifier: + - value: e23c7006-1a13-4211-8920-47548641e574 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6012-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_1_sample_2_subject + identifier: + - value: TCGA-CN-6012-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9023c9bf-02a0-4396-8161-304089957b62 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_2_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_2_diagnosis_0 + identifier: + - value: 40954a8e-e4c2-5604-937b-0a79ac7489d2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_2 + identifier: + - value: 55f96a9c-e2c8-4243-8a7e-94bc6fab73a6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7261 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20992 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_2_sample_0 + identifier: + - value: 69a89590-eb61-41d5-b33e-e7bc5adb92bf + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7261-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_2_sample_0_subject + identifier: + - value: TCGA-CV-7261-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 55f96a9c-e2c8-4243-8a7e-94bc6fab73a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_2_sample_1 + identifier: + - value: b069c55b-496a-4a57-a507-1b2e1b4201ae + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7261-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_2_sample_1_subject + identifier: + - value: TCGA-CV-7261-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 55f96a9c-e2c8-4243-8a7e-94bc6fab73a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_2_sample_2 + identifier: + - value: 00f7bc3c-c0e7-42bf-84d7-87a8a539bd4a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7261-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_2_sample_2_subject + identifier: + - value: TCGA-CV-7261-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 55f96a9c-e2c8-4243-8a7e-94bc6fab73a6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_2_sample_3 + identifier: + - value: a7692585-a129-4671-bfe5-98342a326776 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7261-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_2_sample_3_subject + identifier: + - value: TCGA-CV-7261-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 55f96a9c-e2c8-4243-8a7e-94bc6fab73a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_3_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_3_diagnosis_0 + identifier: + - value: 48e8dd81-ed4d-5c54-af66-84e86477d5c8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_3 + identifier: + - value: c9a36eb5-ac3e-424e-bc2e-303de7105957 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A6DL + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21886 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_3_sample_0 + identifier: + - value: bd90f967-84dd-48cd-aec0-9de9a76df7a9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DL-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_3_sample_0_subject + identifier: + - value: TCGA-BA-A6DL-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c9a36eb5-ac3e-424e-bc2e-303de7105957 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 228 + unit: + coding: *id001 + quantity_collected: + value_decimal: 140 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_3_sample_1 + identifier: + - value: 256469d0-5f36-4966-bf4f-3b4297e55f43 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DL-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_3_sample_1_subject + identifier: + - value: TCGA-BA-A6DL-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c9a36eb5-ac3e-424e-bc2e-303de7105957 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 228 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_3_sample_2 + identifier: + - value: dc102dcf-3f48-49e2-8a6f-cfdc34f8ed0f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DL-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_3_sample_2_subject + identifier: + - value: TCGA-BA-A6DL-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c9a36eb5-ac3e-424e-bc2e-303de7105957 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_4_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_4_diagnosis_0 + identifier: + - value: 1da5c51a-ee25-51a6-a4c2-27d8fdcbe24e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_4 + identifier: + - value: 4cffea0b-90a7-4c86-a73f-bb8feca3ada7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5365 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14190 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_4_sample_0 + identifier: + - value: 1ed245de-fea4-42c9-9197-773bcd12d2a8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5365-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_4_sample_0_subject + identifier: + - value: TCGA-CN-5365-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4cffea0b-90a7-4c86-a73f-bb8feca3ada7 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_4_sample_1 + identifier: + - value: 665d66ad-54ee-478e-bdd0-85d77980fb3e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5365-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_4_sample_1_subject + identifier: + - value: TCGA-CN-5365-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4cffea0b-90a7-4c86-a73f-bb8feca3ada7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_4_sample_2 + identifier: + - value: 665d4bff-603c-497b-816f-c98784665d0f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5365-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_4_sample_2_subject + identifier: + - value: TCGA-CN-5365-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4cffea0b-90a7-4c86-a73f-bb8feca3ada7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_5_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_5_diagnosis_0 + identifier: + - value: d852d062-d7e0-559b-8492-da2b0abe8415 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_5 + identifier: + - value: cd032ddb-55f2-4c77-8dcf-e4e630f7de6f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6470 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14133 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2007-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_5_sample_0 + identifier: + - value: aa121605-a2c9-43fc-a836-8ec6c42b99de + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6470-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_5_sample_0_subject + identifier: + - value: TCGA-CR-6470-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cd032ddb-55f2-4c77-8dcf-e4e630f7de6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_5_sample_1 + identifier: + - value: afb7ea63-2959-4e53-95ea-7a032dcb5a8b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6470-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_5_sample_1_subject + identifier: + - value: TCGA-CR-6470-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cd032ddb-55f2-4c77-8dcf-e4e630f7de6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_6_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_6_diagnosis_0 + identifier: + - value: 47de90b5-a5ed-5ce0-ada8-7f2c8e621913 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_6 + identifier: + - value: 600d5316-b795-4ab2-86fc-52835059386f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A641 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17454 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_6_sample_0 + identifier: + - value: 0c14d932-3b44-48fa-8974-db6e01464851 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A641-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_6_sample_0_subject + identifier: + - value: TCGA-CN-A641-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 600d5316-b795-4ab2-86fc-52835059386f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 346 + unit: + coding: *id001 + quantity_collected: + value_decimal: 130 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_6_sample_1 + identifier: + - value: cc3866fe-2690-4354-a548-10189054b85d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A641-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_6_sample_1_subject + identifier: + - value: TCGA-CN-A641-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 600d5316-b795-4ab2-86fc-52835059386f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 346 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_6_sample_2 + identifier: + - value: 744cbf84-554d-4cba-aa4f-4c1e5e28a1ee + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A641-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_6_sample_2_subject + identifier: + - value: TCGA-CN-A641-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 600d5316-b795-4ab2-86fc-52835059386f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_7_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_7_diagnosis_0 + identifier: + - value: 0584ee86-f589-5812-9bad-03855a31693b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_7 + identifier: + - value: 7de19081-d5fd-468c-ad0d-f6e3e8b2ad70 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-4076 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14405 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2003-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_7_sample_0 + identifier: + - value: d6f48bb2-379a-448d-b13d-2dfc5da91d0c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-4076-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_7_sample_0_subject + identifier: + - value: TCGA-BA-4076-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7de19081-d5fd-468c-ad0d-f6e3e8b2ad70 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_7_sample_1 + identifier: + - value: fd99fd83-4040-4738-8a5a-e42d36ecfe0e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-4076-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_7_sample_1_subject + identifier: + - value: TCGA-BA-4076-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7de19081-d5fd-468c-ad0d-f6e3e8b2ad70 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_7_sample_2 + identifier: + - value: 5fe1ae56-74a5-44a9-b8d1-7f05a569bb34 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-4076-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_7_sample_2_subject + identifier: + - value: TCGA-BA-4076-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7de19081-d5fd-468c-ad0d-f6e3e8b2ad70 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_8_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_8_diagnosis_0 + identifier: + - value: 5202e65a-e9af-58ee-8960-9190089fb197 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_8 + identifier: + - value: 89f91e36-fed8-4da3-8a35-c761d6f65285 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6467 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21689 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_8_sample_0 + identifier: + - value: 2d9ad43c-f177-455e-9b63-1b9ffdc672d9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6467-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_8_sample_0_subject + identifier: + - value: TCGA-CR-6467-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 89f91e36-fed8-4da3-8a35-c761d6f65285 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_8_sample_1 + identifier: + - value: 5ef4d047-5a84-4e03-acf5-02029d8a4cf2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6467-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_8_sample_1_subject + identifier: + - value: TCGA-CR-6467-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 89f91e36-fed8-4da3-8a35-c761d6f65285 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_9_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_9_diagnosis_0 + identifier: + - value: 0a622048-699a-55f4-ba31-6c9e95e1cabd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_9 + identifier: + - value: a8a391ba-e595-4a91-bd55-02b312e55427 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-DQ-7590 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18718 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_9_sample_0 + identifier: + - value: 36fb3f52-714b-4b86-a7a5-ca4b017fd182 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7590-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_9_sample_0_subject + identifier: + - value: TCGA-DQ-7590-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a8a391ba-e595-4a91-bd55-02b312e55427 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_9_sample_1 + identifier: + - value: 95018dba-f23d-4af0-b774-c28be60007f7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7590-10D + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_9_sample_1_subject + identifier: + - value: TCGA-DQ-7590-10D + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a8a391ba-e595-4a91-bd55-02b312e55427 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 797 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_9_sample_2 + identifier: + - value: b8eb9edb-fce8-4e72-9cbf-c4868c04965c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7590-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_9_sample_2_subject + identifier: + - value: TCGA-DQ-7590-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a8a391ba-e595-4a91-bd55-02b312e55427 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_10_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_10_diagnosis_0 + identifier: + - value: b23327de-182a-555c-9323-77d5bd3dd453 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_10 + identifier: + - value: f22eac21-8a74-433a-b65c-3540d14a45cb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7415 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22062 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1995-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_10_sample_0 + identifier: + - value: 72f5520a-28f0-4be6-afe0-6bee4de5b69a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7415-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_10_sample_0_subject + identifier: + - value: TCGA-CV-7415-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f22eac21-8a74-433a-b65c-3540d14a45cb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_10_sample_1 + identifier: + - value: 106c7016-9bf6-415a-a0fc-3722a1aaf2c6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7415-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_10_sample_1_subject + identifier: + - value: TCGA-CV-7415-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f22eac21-8a74-433a-b65c-3540d14a45cb + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_10_sample_2 + identifier: + - value: b7d03ca7-f518-4587-a54f-03896e53b167 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7415-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_10_sample_2_subject + identifier: + - value: TCGA-CV-7415-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f22eac21-8a74-433a-b65c-3540d14a45cb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_11_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_11_diagnosis_0 + identifier: + - value: 7c0c3290-5b41-50b4-b37d-536ebbac2af8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_11 + identifier: + - value: 241d9310-9137-42dd-b28d-0dc50c44cb43 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7101 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 29550 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_11_sample_0 + identifier: + - value: 8e461b7f-1bfd-476d-a948-7aadb89a41e5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7101-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_11_sample_0_subject + identifier: + - value: TCGA-CV-7101-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 241d9310-9137-42dd-b28d-0dc50c44cb43 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_11_sample_1 + identifier: + - value: 79ec5357-3a44-40db-a1ba-ee282b484526 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7101-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_11_sample_1_subject + identifier: + - value: TCGA-CV-7101-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 241d9310-9137-42dd-b28d-0dc50c44cb43 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_11_sample_2 + identifier: + - value: 397b08f6-f560-418b-a6e6-2d953187bd5d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7101-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_11_sample_2_subject + identifier: + - value: TCGA-CV-7101-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 241d9310-9137-42dd-b28d-0dc50c44cb43 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_11_sample_3 + identifier: + - value: f040a5a4-e955-4e69-9f2e-ae9a4c78780a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7101-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_11_sample_3_subject + identifier: + - value: TCGA-CV-7101-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 241d9310-9137-42dd-b28d-0dc50c44cb43 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_12_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_12_diagnosis_0 + identifier: + - value: cf36baf2-10e8-523f-9dd9-0f9c938be574 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_12 + identifier: + - value: 05f01280-bf77-4682-a7a8-20dd0eac77bd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-4223 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17608 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2003-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_12_sample_0 + identifier: + - value: 3285f0ab-61e2-4235-b0ac-af1718ca1874 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4223-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_12_sample_0_subject + identifier: + - value: TCGA-BB-4223-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 05f01280-bf77-4682-a7a8-20dd0eac77bd + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_12_sample_1 + identifier: + - value: 82db742d-885d-4788-b509-474715ae183b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4223-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_12_sample_1_subject + identifier: + - value: TCGA-BB-4223-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 05f01280-bf77-4682-a7a8-20dd0eac77bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_12_sample_2 + identifier: + - value: 75430612-09bb-4d6f-9304-62a5b517d424 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4223-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_12_sample_2_subject + identifier: + - value: TCGA-BB-4223-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 05f01280-bf77-4682-a7a8-20dd0eac77bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_13_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_13_diagnosis_0 + identifier: + - value: bd3b2bda-4737-50bb-863a-334134a31156 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_13 + identifier: + - value: 86a5c819-49e9-4b06-b43d-0f0c06a935fd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A8ZA + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21979 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_13_sample_0 + identifier: + - value: 4db7e146-bf2a-4729-ae80-d471370b62a0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8ZA-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_13_sample_0_subject + identifier: + - value: TCGA-QK-A8ZA-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 86a5c819-49e9-4b06-b43d-0f0c06a935fd + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_13_sample_1 + identifier: + - value: 9adfbc71-da3c-4a8e-a72f-76690e90a8ca + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8ZA-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_13_sample_1_subject + identifier: + - value: TCGA-QK-A8ZA-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 86a5c819-49e9-4b06-b43d-0f0c06a935fd + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 35 + unit: + coding: *id001 + quantity_collected: + value_decimal: 30 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_13_sample_2 + identifier: + - value: f92383bc-5869-44d6-a128-60b60043d778 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8ZA-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_13_sample_2_subject + identifier: + - value: TCGA-QK-A8ZA-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 86a5c819-49e9-4b06-b43d-0f0c06a935fd + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 35 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_14_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_14_diagnosis_0 + identifier: + - value: 3ef5f7db-6234-5c11-96d5-fdb6cf8ad63e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_14 + identifier: + - value: e16e9535-b20f-4c9a-8b5b-82df80c99448 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5978 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19480 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_14_sample_0 + identifier: + - value: b33eba98-6a89-4454-9a53-94999cd5003c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5978-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_14_sample_0_subject + identifier: + - value: TCGA-CV-5978-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e16e9535-b20f-4c9a-8b5b-82df80c99448 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_14_sample_1 + identifier: + - value: 7560ec6d-e0f2-4b55-88bf-62e7173126a1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5978-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_14_sample_1_subject + identifier: + - value: TCGA-CV-5978-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e16e9535-b20f-4c9a-8b5b-82df80c99448 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_14_sample_2 + identifier: + - value: b801368a-b10a-4a42-bda8-5df8216b532f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5978-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_14_sample_2_subject + identifier: + - value: TCGA-CV-5978-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e16e9535-b20f-4c9a-8b5b-82df80c99448 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_15_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_15_diagnosis_0 + identifier: + - value: c5df4db4-06f3-4596-98d2-3ab0e5df45b6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_15 + identifier: + - value: bb3f728d-c9b3-4cc9-941d-d3e77dffa196 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003711 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_15_sample_0 + identifier: + - value: 7eef7c3e-d42d-4cf5-9ad1-3099b828f776 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003711-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_15_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003711-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: bb3f728d-c9b3-4cc9-941d-d3e77dffa196 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_16_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_16_diagnosis_0 + identifier: + - value: 0bf30179-24b0-4b0e-856d-7226a72eb3e0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_16 + identifier: + - value: e1adae15-f45a-4c4d-b77c-e8a30741d2cf + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-052973 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_16_sample_0 + identifier: + - value: b39fb248-8053-47b7-aa2c-d69335f218ce + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-052973-173599 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_16_sample_0_subject + identifier: + - value: GENIE-DFCI-052973-173599 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e1adae15-f45a-4c4d-b77c-e8a30741d2cf + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_17_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_17_diagnosis_0 + identifier: + - value: cb7a6350-80e2-4b6e-9b86-05632255db52 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_17 + identifier: + - value: e3262bc8-cda5-4506-a0b6-17bbf08c5cab + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003213 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_17_sample_0 + identifier: + - value: a764b89e-ad60-4316-a812-24a5eec7b9dd + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003213-4767 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_17_sample_0_subject + identifier: + - value: GENIE-DFCI-003213-4767 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e3262bc8-cda5-4506-a0b6-17bbf08c5cab + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_18_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_18_diagnosis_0 + identifier: + - value: 64ba1bbd-bf72-4700-97be-0bc054876c84 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_18 + identifier: + - value: bfd25bfd-f31f-4ce2-91d0-1a1e5b27c0e2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005062 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_18_sample_0 + identifier: + - value: a0deb101-019f-46d7-8cb2-ee98c9d7aa92 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005062-1372 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_18_sample_0_subject + identifier: + - value: GENIE-DFCI-005062-1372 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: bfd25bfd-f31f-4ce2-91d0-1a1e5b27c0e2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_19_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_19_diagnosis_0 + identifier: + - value: 6759d804-a7db-43ed-a3ae-db633fdc7cdb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_19 + identifier: + - value: 3e6b8e68-126f-4ab3-8b7a-59204f0f75a8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010241 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_19_sample_0 + identifier: + - value: 856fab11-14d9-4e8c-af8a-65684ca39418 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010241-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_19_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010241-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3e6b8e68-126f-4ab3-8b7a-59204f0f75a8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_20_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_20_diagnosis_0 + identifier: + - value: d55686fe-0423-4b01-9719-ade00bed3004 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_20 + identifier: + - value: 499f7e32-7bab-48d7-b05b-424faa7a8fc2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0009761 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_20_sample_0 + identifier: + - value: 64dd4e81-f01b-4846-b306-20b7cd7d9340 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0009761-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_20_sample_0_subject + identifier: + - value: GENIE-MSK-P-0009761-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 499f7e32-7bab-48d7-b05b-424faa7a8fc2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_21_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_21_diagnosis_0 + identifier: + - value: 30984445-18bb-4b5a-be50-8bed548e6e00 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_21 + identifier: + - value: 56be5106-965c-436b-baff-3e94b0f00970 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007662 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_21_sample_0 + identifier: + - value: 46f8b134-ad13-42d1-b3c7-6b2d8cf77f90 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007662-3905 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_21_sample_0_subject + identifier: + - value: GENIE-DFCI-007662-3905 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 56be5106-965c-436b-baff-3e94b0f00970 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_22_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_22_diagnosis_0 + identifier: + - value: 32bc08a5-7441-4dfc-b13c-9e193e5a7ac9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_22 + identifier: + - value: 6bf510b6-4ec4-422c-a733-85c715949779 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001682 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_22_sample_0 + identifier: + - value: b2a64027-92cc-4961-9c27-821fff58c5ca + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001682-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_22_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001682-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6bf510b6-4ec4-422c-a733-85c715949779 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_23_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_23_diagnosis_0 + identifier: + - value: 8d28ba70-052a-42c0-9a4e-f06ea143f381 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_23 + identifier: + - value: 76821865-0bc4-4024-b13d-898700c2cfa1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001195 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_23_sample_0 + identifier: + - value: b857d450-dfaf-4407-84e8-d3bbf843cbc3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001195-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_23_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001195-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 76821865-0bc4-4024-b13d-898700c2cfa1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_24_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_24_diagnosis_0 + identifier: + - value: fb0593eb-d74f-436d-9bc3-37f8d8285296 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_24 + identifier: + - value: 09e7a724-94d3-4f53-9f3a-0564b51f7c98 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009648 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_24_sample_0 + identifier: + - value: 3c02ad20-11ec-4e71-b7e8-c29194ae502f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009648-9028 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_24_sample_0_subject + identifier: + - value: GENIE-DFCI-009648-9028 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 09e7a724-94d3-4f53-9f3a-0564b51f7c98 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_25_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_25_diagnosis_0 + identifier: + - value: 915d0d2e-63da-4723-909a-4bece5afab90 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_25 + identifier: + - value: 8ede4376-d058-446b-a591-14c3c0bfdd96 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0018175 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_25_sample_0 + identifier: + - value: d4ba57ac-0820-4d57-85a6-06122bb4559e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0018175-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_25_sample_0_subject + identifier: + - value: GENIE-MSK-P-0018175-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8ede4376-d058-446b-a591-14c3c0bfdd96 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_26_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_26_diagnosis_0 + identifier: + - value: b0f16df9-9556-4ff1-b8b8-afabece2fd14 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_26 + identifier: + - value: f962e7ed-e5d8-4092-93c9-ab8a0f68dac8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-UHN-071596 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_26_sample_0 + identifier: + - value: 5cdc6f40-9b5f-4dc0-9082-a9500c3e5af4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-UHN-071596-ARC1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_26_sample_0_subject + identifier: + - value: GENIE-UHN-071596-ARC1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f962e7ed-e5d8-4092-93c9-ab8a0f68dac8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_27_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_27_diagnosis_0 + identifier: + - value: 07feaa02-95ec-48b9-83ff-ddd765c8ca9d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_27 + identifier: + - value: 3ff9b247-a2ba-4ab3-a92c-5f356efef969 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0006098 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_27_sample_0 + identifier: + - value: eca4b442-f9d1-4018-94cb-158757bd3bea + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0006098-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_27_sample_0_subject + identifier: + - value: GENIE-MSK-P-0006098-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3ff9b247-a2ba-4ab3-a92c-5f356efef969 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_28_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_28_diagnosis_0 + identifier: + - value: 81d9c62a-5f07-4409-aad8-4f9e02b90669 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_28 + identifier: + - value: 6bc9bb4c-c791-4f88-b00e-3aaaa06b54a0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015745 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_28_sample_0 + identifier: + - value: cd31b18a-5019-4a94-8966-a1160e544684 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015745-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_28_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015745-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6bc9bb4c-c791-4f88-b00e-3aaaa06b54a0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_29_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_29_diagnosis_0 + identifier: + - value: 78daf8d2-f74b-4d9e-9ffe-79e90425ad3c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_29 + identifier: + - value: 2f3b0871-8878-46df-9340-d33c6ca72220 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD7638 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 13024 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Adenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8140/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_29_sample_0 + identifier: + - value: a4ae0499-714f-4d0b-95b5-e085bb652117 + system: http://crdc.nci.nih.gov/gdc + - value: AD7638_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_29_sample_0_subject + identifier: + - value: AD7638_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2f3b0871-8878-46df-9340-d33c6ca72220 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_30_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_30_diagnosis_0 + identifier: + - value: 36009b16-600e-42f9-9509-783c76c5b88d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_30 + identifier: + - value: 1c6adf10-b25a-406a-a765-663a16d0b469 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-034499 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_30_sample_0 + identifier: + - value: bce047a2-b5b7-4ccf-8bf9-406d8c87d7a3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-034499-159099 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_30_sample_0_subject + identifier: + - value: GENIE-DFCI-034499-159099 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1c6adf10-b25a-406a-a765-663a16d0b469 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_31_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_31_diagnosis_0 + identifier: + - value: 4c3c3952-6e85-4fd3-bc05-81c91ce3faef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_31 + identifier: + - value: 7009a92e-d3bf-432d-a8bf-96f6ba5cbee0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003978 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_31_sample_0 + identifier: + - value: 10935163-56ad-43d1-af91-1846aa5922eb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003978-789 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_31_sample_0_subject + identifier: + - value: GENIE-DFCI-003978-789 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7009a92e-d3bf-432d-a8bf-96f6ba5cbee0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_32_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_32_diagnosis_0 + identifier: + - value: a84b9519-37b2-4311-ac32-8151ae7261e7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_32 + identifier: + - value: b5729776-69f7-40e1-b576-6d16399e85f8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-090167 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_32_sample_0 + identifier: + - value: 0f1ec484-9205-42f4-9696-815dae75b073 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-090167-282584 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_32_sample_0_subject + identifier: + - value: GENIE-DFCI-090167-282584 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b5729776-69f7-40e1-b576-6d16399e85f8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_33_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_33_diagnosis_0 + identifier: + - value: 65645e51-3cea-4c45-a029-ecd7cef6c8ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_33 + identifier: + - value: 0fba887e-8b57-40e8-8661-311b6e268d10 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-001639 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_33_sample_0 + identifier: + - value: b1a851b3-94bf-4652-82d3-cc6133cd1565 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-001639-6186 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_33_sample_0_subject + identifier: + - value: GENIE-DFCI-001639-6186 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0fba887e-8b57-40e8-8661-311b6e268d10 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_34_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_34_diagnosis_0 + identifier: + - value: ad86791e-dc2b-4a82-9c74-674bc6baf268 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_34 + identifier: + - value: 9cf2460d-cac1-4c8b-b201-c38c05eb9965 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009352 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_34_sample_0 + identifier: + - value: 5e386079-a9c2-4c7e-80ed-9dda270249b9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009352-7151 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_34_sample_0_subject + identifier: + - value: GENIE-DFCI-009352-7151 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9cf2460d-cac1-4c8b-b201-c38c05eb9965 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_35_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_35_diagnosis_0 + identifier: + - value: c9269eb1-ab75-4719-8cd9-e9efd32f7d7e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_35 + identifier: + - value: 46bea724-e121-4100-acde-2e9d8eb2da2b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-5245 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_35_sample_0 + identifier: + - value: 08209047-3b7a-4295-90b0-ddc92aa1e1c9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-5245-16353 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_35_sample_0_subject + identifier: + - value: GENIE-MDA-5245-16353 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 46bea724-e121-4100-acde-2e9d8eb2da2b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_36_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_36_diagnosis_0 + identifier: + - value: 18d11972-ed5f-4c5b-9511-18b00bca7f7d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_36 + identifier: + - value: b2d063d0-81ad-4d5d-aeb4-be05e6aa32bc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-8036 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_36_sample_0 + identifier: + - value: 475098e0-9927-42fc-adf2-e280d8aec3bb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-8036-18260 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_36_sample_0_subject + identifier: + - value: GENIE-MDA-8036-18260 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b2d063d0-81ad-4d5d-aeb4-be05e6aa32bc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_37_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_37_diagnosis_0 + identifier: + - value: 8c624d17-a588-40ee-9902-ed694d794814 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_37 + identifier: + - value: f4f3fb03-f084-4679-8f29-bf3e7e5a5349 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD1281 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18738 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_37_sample_0 + identifier: + - value: a1fe6dde-024f-4487-8838-24fda3505cc3 + system: http://crdc.nci.nih.gov/gdc + - value: AD1281_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_37_sample_0_subject + identifier: + - value: AD1281_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f4f3fb03-f084-4679-8f29-bf3e7e5a5349 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_38_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_38_diagnosis_0 + identifier: + - value: 1fe06c82-aa43-44ac-a091-8dec17e796ba + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_38 + identifier: + - value: 90f91f69-ff95-4df4-b6e0-26f446d232c5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037687 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_38_sample_0 + identifier: + - value: 98e2382a-2d7b-445d-83ff-1dc53d66db12 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037687-158970 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_38_sample_0_subject + identifier: + - value: GENIE-DFCI-037687-158970 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 90f91f69-ff95-4df4-b6e0-26f446d232c5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_39_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_39_diagnosis_0 + identifier: + - value: 2326f9b7-e2e8-487a-acd4-b00bc9967a8e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_39 + identifier: + - value: 6f76c66d-eb63-4118-9dda-4f3dc750875d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-6597 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_39_sample_0 + identifier: + - value: 35f0c152-0c87-42bb-a1b7-b306e66514f5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-6597-17790 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_39_sample_0_subject + identifier: + - value: GENIE-MDA-6597-17790 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6f76c66d-eb63-4118-9dda-4f3dc750875d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_40_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_40_diagnosis_0 + identifier: + - value: d7d13cee-ba1b-4e36-a0a5-3f925c871020 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_40 + identifier: + - value: 31991373-6aa0-45be-be42-2a58d63677e4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0013833 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_40_sample_0 + identifier: + - value: b6ddcf15-8ecb-47ca-bb29-60b9b43fa7aa + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0013833-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_40_sample_0_subject + identifier: + - value: GENIE-MSK-P-0013833-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 31991373-6aa0-45be-be42-2a58d63677e4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_41_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_41_diagnosis_0 + identifier: + - value: e71fe2d8-2dc3-45b4-bc48-25b118a6f909 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_41 + identifier: + - value: 7863612b-6350-4aa8-8d4b-e5f384ef7456 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD2206 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14547 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_41_sample_0 + identifier: + - value: 68742842-28e9-49db-b49d-79c73ad4ef0c + system: http://crdc.nci.nih.gov/gdc + - value: AD2206_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_41_sample_0_subject + identifier: + - value: AD2206_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7863612b-6350-4aa8-8d4b-e5f384ef7456 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_42_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_42_diagnosis_0 + identifier: + - value: 20b2ca7d-bce3-44c1-a0db-ef271aca97bc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_42 + identifier: + - value: 7213db8b-2163-43a6-b62b-5e0df28317ac + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD2717 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15088 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_42_sample_0 + identifier: + - value: 69907c44-c952-482a-a307-44efd82a16dd + system: http://crdc.nci.nih.gov/gdc + - value: AD2717_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_42_sample_0_subject + identifier: + - value: AD2717_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7213db8b-2163-43a6-b62b-5e0df28317ac + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_43_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_43_diagnosis_0 + identifier: + - value: ca8d9936-f4d9-465a-8640-66a91f735a60 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_43 + identifier: + - value: 459de74d-b512-47ed-a5ce-1a5f2a739579 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0018419 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_43_sample_0 + identifier: + - value: 60efb1a2-a8b1-40a7-b230-e4b532a8048b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0018419-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_43_sample_0_subject + identifier: + - value: GENIE-MSK-P-0018419-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 459de74d-b512-47ed-a5ce-1a5f2a739579 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_44_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_44_diagnosis_0 + identifier: + - value: d0678ad6-4a4a-4ec8-9e5f-352c1347efc2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_44 + identifier: + - value: 33fa625e-852e-49ef-8134-6ea46edb5183 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-a8pxs0u6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_44_sample_0 + identifier: + - value: ab9d819a-6445-4bad-a520-3d1edf413508 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-a8pxs0u6-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_44_sample_0_subject + identifier: + - value: GENIE-GRCC-a8pxs0u6-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 33fa625e-852e-49ef-8134-6ea46edb5183 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_45_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_45_diagnosis_0 + identifier: + - value: cac9736c-3015-486b-b69a-906d2bcbac13 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_45 + identifier: + - value: ab01636f-53b0-4026-b9ca-bfa48e77d83a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-a20580bb + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_45_sample_0 + identifier: + - value: cf3feb17-3b74-4d84-8395-c4af9b8f4514 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-a20580bb-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_45_sample_0_subject + identifier: + - value: GENIE-GRCC-a20580bb-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ab01636f-53b0-4026-b9ca-bfa48e77d83a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_46_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_46_diagnosis_0 + identifier: + - value: b5616ad7-8322-44c9-8b64-01314decc5a5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_46 + identifier: + - value: d420a07e-e0b6-4ff7-8ba7-c7a378edbf0d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-9df16b49 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_46_sample_0 + identifier: + - value: 3dc819bf-5af3-4be1-a892-974d670975c9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-9df16b49-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_46_sample_0_subject + identifier: + - value: GENIE-GRCC-9df16b49-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d420a07e-e0b6-4ff7-8ba7-c7a378edbf0d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_47_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_47_diagnosis_0 + identifier: + - value: fcd7326c-3bf2-425a-b117-f1e5f6910db9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_47 + identifier: + - value: cbe180e4-87bf-4574-952e-ba3d0c8cd70c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-c9c06784 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_47_sample_0 + identifier: + - value: 43bdb66c-6b5a-4a1c-9d44-2717ecc981ed + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-c9c06784-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_47_sample_0_subject + identifier: + - value: GENIE-GRCC-c9c06784-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cbe180e4-87bf-4574-952e-ba3d0c8cd70c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_48_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_48_diagnosis_0 + identifier: + - value: 640dafcd-ca8f-4305-bd40-240ff476b75e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_48 + identifier: + - value: 469109f7-ce07-4bc8-9262-0157cd2585c4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006707 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_48_sample_0 + identifier: + - value: 53e7103c-42c4-41cc-948c-b8e23271bee9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006707-2784 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_48_sample_0_subject + identifier: + - value: GENIE-DFCI-006707-2784 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 469109f7-ce07-4bc8-9262-0157cd2585c4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_49_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_49_diagnosis_0 + identifier: + - value: 6307ff41-9bb5-438d-8789-a73b41303d64 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_49 + identifier: + - value: b06cab31-2dde-4880-8cbf-a33ccf75abb2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-036509 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_49_sample_0 + identifier: + - value: ba40b824-5fe9-4a73-b7f0-9b371af64f65 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-036509-75021 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_49_sample_0_subject + identifier: + - value: GENIE-DFCI-036509-75021 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b06cab31-2dde-4880-8cbf-a33ccf75abb2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_50_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_50_diagnosis_0 + identifier: + - value: 4c9f5000-dbac-4497-b434-57036c18a022 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_50 + identifier: + - value: 9e817deb-9dbf-445f-9bb1-0f27a90f2eed + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008669 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_50_sample_0 + identifier: + - value: c0927894-b73f-4930-b147-e079caeb60e5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008669-7093 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_50_sample_0_subject + identifier: + - value: GENIE-DFCI-008669-7093 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9e817deb-9dbf-445f-9bb1-0f27a90f2eed + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_51_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_51_diagnosis_0 + identifier: + - value: 60d7b883-bf64-4777-9f6a-efaf4c4a40c4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_51 + identifier: + - value: 6881d9bc-5ff2-46d1-99ef-aa27dd34bd78 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003875 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_51_sample_0 + identifier: + - value: c930148f-2059-480b-960a-4efcb3c98ac1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003875-1298 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_51_sample_0_subject + identifier: + - value: GENIE-DFCI-003875-1298 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6881d9bc-5ff2-46d1-99ef-aa27dd34bd78 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_52_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_52_diagnosis_0 + identifier: + - value: 094085f3-01f3-4992-b559-832c897a704f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_52 + identifier: + - value: 2accfda2-ed5a-4903-949d-c0522a68b9b1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003374 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_52_sample_0 + identifier: + - value: e868826f-a629-4839-bc5f-5383b74aac12 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003374-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_52_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003374-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2accfda2-ed5a-4903-949d-c0522a68b9b1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_53_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_53_diagnosis_0 + identifier: + - value: 5ddc8873-1487-4787-8a1d-3b116a2db42a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_53 + identifier: + - value: b37089d4-c86e-44da-aab4-624f4163c014 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010816 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_53_sample_0 + identifier: + - value: e179e193-0933-48cd-98fe-aa4e21c0ad44 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010816-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_53_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010816-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b37089d4-c86e-44da-aab4-624f4163c014 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_54_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_54_diagnosis_0 + identifier: + - value: 605addeb-a295-4bd2-ab90-347c41e9b1ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_54 + identifier: + - value: 0a81deef-fb14-4a98-be3e-ddf56fbefdf5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008105 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_54_sample_0 + identifier: + - value: b9b1b672-a788-46eb-bc8e-a5b401d1a430 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008105-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_54_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008105-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0a81deef-fb14-4a98-be3e-ddf56fbefdf5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_55_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_55_diagnosis_0 + identifier: + - value: 5a82f834-a2f8-4d61-a816-c410213556b4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_55 + identifier: + - value: 93e68d18-300c-4371-b33b-0e941c7f728a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000319 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_55_sample_0 + identifier: + - value: d0ef535c-d0ed-471d-a1a6-3cf9600d37cb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000319-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_55_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000319-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 93e68d18-300c-4371-b33b-0e941c7f728a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_56_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_56_diagnosis_0 + identifier: + - value: bf8ae40c-068c-44c4-b09e-954969e83369 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_56 + identifier: + - value: 9cc331f6-c88d-48ff-b352-4efbcecac5c5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0016039 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_56_sample_0 + identifier: + - value: ab79d569-bc64-4639-a6a8-74bc2bbe0d0c + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0016039-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_56_sample_0_subject + identifier: + - value: GENIE-MSK-P-0016039-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9cc331f6-c88d-48ff-b352-4efbcecac5c5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_57_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_57_diagnosis_0 + identifier: + - value: c1dc41f5-0fea-42e8-afdb-fabc542d0548 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_57 + identifier: + - value: 9b3854dc-97d8-4cf0-bde7-626798755e49 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0005869 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_57_sample_0 + identifier: + - value: bb6ae997-ee6b-42e0-ab0c-c9fbc64f8d9b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0005869-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_57_sample_0_subject + identifier: + - value: GENIE-MSK-P-0005869-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9b3854dc-97d8-4cf0-bde7-626798755e49 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_58_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_58_diagnosis_0 + identifier: + - value: 6fdc7de3-3d2e-459a-94ea-1dba9572f47d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_58 + identifier: + - value: 2ddc7263-1685-49fe-af57-26e9619c2ca8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-480293 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_58_sample_0 + identifier: + - value: 116b69cf-c9f3-45c6-be86-c4f22a36dcf8 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-480293-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_58_sample_0_subject + identifier: + - value: GENIE-VICC-480293-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2ddc7263-1685-49fe-af57-26e9619c2ca8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_59_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_59_diagnosis_0 + identifier: + - value: c70dbc51-07bb-49a1-bffc-ea639cf09e66 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_59 + identifier: + - value: 11638c5b-6704-4814-ba91-5dd33f8572a0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5893 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22346 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_59_sample_0 + identifier: + - value: 3c1903f3-2a52-46cf-872e-060ba3a092e3 + system: http://crdc.nci.nih.gov/gdc + - value: AD5893_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_59_sample_0_subject + identifier: + - value: AD5893_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 11638c5b-6704-4814-ba91-5dd33f8572a0 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_60_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_60_diagnosis_0 + identifier: + - value: ae2f70f2-dd19-493b-b6ea-bbe2cbe507cd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_60 + identifier: + - value: 927957f5-c14c-427c-a49c-bbc0a1572b54 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0014898 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_60_sample_0 + identifier: + - value: d7332e8a-d17d-497f-9b44-cc7992f48739 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0014898-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_60_sample_0_subject + identifier: + - value: GENIE-MSK-P-0014898-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 927957f5-c14c-427c-a49c-bbc0a1572b54 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_61_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_61_diagnosis_0 + identifier: + - value: 9d41e68e-c648-42ea-9320-6e08b9b5dd4c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_61 + identifier: + - value: 8fe9b700-cc26-4077-8d1e-819390c91b17 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007598 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_61_sample_0 + identifier: + - value: 87d18b2c-1241-43b3-b7aa-24442a047ade + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007598-4084 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_61_sample_0_subject + identifier: + - value: GENIE-DFCI-007598-4084 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8fe9b700-cc26-4077-8d1e-819390c91b17 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_62_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_62_diagnosis_0 + identifier: + - value: 2b051980-b5b7-4b1d-900c-9705c24b2a78 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_62 + identifier: + - value: 38de40ea-679f-45fb-acbd-152f69c75ac8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009287 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_62_sample_0 + identifier: + - value: 781e0bea-f234-496c-915c-c163fc8de24b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009287-6605 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_62_sample_0_subject + identifier: + - value: GENIE-DFCI-009287-6605 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 38de40ea-679f-45fb-acbd-152f69c75ac8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_63_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_63_diagnosis_0 + identifier: + - value: d2b0be44-b12f-443f-9d48-3e26ea1ed386 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_63 + identifier: + - value: 3ff2bdac-52ab-4b33-becd-730df42ec5bf + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD7867 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21298 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_63_sample_0 + identifier: + - value: 1fc039e3-94d1-4fe2-9d51-796dce543f9f + system: http://crdc.nci.nih.gov/gdc + - value: AD7867_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_63_sample_0_subject + identifier: + - value: AD7867_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3ff2bdac-52ab-4b33-becd-730df42ec5bf + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_64_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_64_diagnosis_0 + identifier: + - value: 6b76278a-cb58-4308-bfef-fa1902a02375 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_64 + identifier: + - value: 2caeafc5-d4b2-4a7f-845b-1cbfa41efc53 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010467 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_64_sample_0 + identifier: + - value: 02cf8f79-3109-423e-b290-9b0cf112e827 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010467-10870 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_64_sample_0_subject + identifier: + - value: GENIE-DFCI-010467-10870 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2caeafc5-d4b2-4a7f-845b-1cbfa41efc53 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_65_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_65_diagnosis_0 + identifier: + - value: 3f9d8932-dc6a-4225-b085-953225ae22ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_65 + identifier: + - value: 969f0d84-e608-46ac-8174-18866c09859f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0007407 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_65_sample_0 + identifier: + - value: cd1a65bd-7bc3-4c1e-9d5e-792938c2fc5a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0007407-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_65_sample_0_subject + identifier: + - value: GENIE-MSK-P-0007407-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 969f0d84-e608-46ac-8174-18866c09859f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_66_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_66_diagnosis_0 + identifier: + - value: d113feec-68eb-4294-b6b4-6b8e22ce56bb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_66 + identifier: + - value: b0c52d5f-7ec9-4b96-976f-107390f9393d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0016562 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_66_sample_0 + identifier: + - value: 99c1a34d-ba04-462f-be28-bb5eac77b316 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0016562-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_66_sample_0_subject + identifier: + - value: GENIE-MSK-P-0016562-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b0c52d5f-7ec9-4b96-976f-107390f9393d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_67_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_67_diagnosis_0 + identifier: + - value: 57e78d94-5a02-499e-953f-e5539884009b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_67 + identifier: + - value: 87f19554-2dfa-45cb-ad53-58372b7cb61c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-036456 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_67_sample_0 + identifier: + - value: 6f3b4fcf-0519-439f-b3e9-6a0678745885 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-036456-74857 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_67_sample_0_subject + identifier: + - value: GENIE-DFCI-036456-74857 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 87f19554-2dfa-45cb-ad53-58372b7cb61c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_68_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_68_diagnosis_0 + identifier: + - value: 25182ec3-0d7b-44ca-82e4-f1a8d7de4a28 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_68 + identifier: + - value: a6dfd56c-787f-4d69-be43-9816be7e4919 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD18004 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 9238 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Adenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8140/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_68_sample_0 + identifier: + - value: b62fca52-48c3-4bea-b5f7-5794a1ed4f43 + system: http://crdc.nci.nih.gov/gdc + - value: AD18004_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_68_sample_0_subject + identifier: + - value: AD18004_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a6dfd56c-787f-4d69-be43-9816be7e4919 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_69_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_69_diagnosis_0 + identifier: + - value: 43aa2ba4-d59e-4e9f-9b1f-009fba8ee08a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_69 + identifier: + - value: f06450b5-3e30-45c4-a86d-30f0861b265b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-4754 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_69_sample_0 + identifier: + - value: c3431e69-82eb-4eef-9e13-312bfde95103 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-4754-15863 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_69_sample_0_subject + identifier: + - value: GENIE-MDA-4754-15863 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f06450b5-3e30-45c4-a86d-30f0861b265b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_70_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_70_diagnosis_0 + identifier: + - value: 3cd3b53e-38ff-454f-8b3a-d7942696429f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_70 + identifier: + - value: b9ab3a6c-633c-4345-9e73-38f51704a77b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015915 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_70_sample_0 + identifier: + - value: f48ed568-6c4b-4746-b480-139ed3ab5794 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015915-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_70_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015915-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b9ab3a6c-633c-4345-9e73-38f51704a77b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_71_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_71_diagnosis_0 + identifier: + - value: c8b3a37f-01ec-481e-9460-0bcac22cc002 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_71 + identifier: + - value: 108a3746-ad40-47ac-a2f3-3f7c74cfaf6c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-18076aef + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_71_sample_0 + identifier: + - value: 960fe012-e237-42c8-a3e0-d02853ce3818 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-18076aef-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_71_sample_0_subject + identifier: + - value: GENIE-GRCC-18076aef-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 108a3746-ad40-47ac-a2f3-3f7c74cfaf6c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_72_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_72_diagnosis_0 + identifier: + - value: 9c1cd7ed-46f5-4809-a898-22cc0e15cd64 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_72 + identifier: + - value: 6155c834-aad3-443f-89dc-20874808ae6b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-438c3609 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_72_sample_0 + identifier: + - value: bc168208-ee4f-4a50-8ddf-b72b0dd59da2 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-438c3609-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_72_sample_0_subject + identifier: + - value: GENIE-GRCC-438c3609-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6155c834-aad3-443f-89dc-20874808ae6b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_73_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_73_diagnosis_0 + identifier: + - value: 25fb47b9-2f00-4140-92bc-462b1e8447c4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_73 + identifier: + - value: a223f7fe-6c67-4136-b297-a8513ffc9ed4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-4wf609jo + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_73_sample_0 + identifier: + - value: 0ef8dcd6-8f67-4f29-a69d-d952df3d43b3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-4wf609jo-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_73_sample_0_subject + identifier: + - value: GENIE-GRCC-4wf609jo-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a223f7fe-6c67-4136-b297-a8513ffc9ed4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_74_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_74_diagnosis_0 + identifier: + - value: fb2076bc-c2ef-4566-ab26-c6c6fcd212ed + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_74 + identifier: + - value: f64a4a61-5d5c-49d3-8552-f3f5eb24e632 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-b3db0c02 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_74_sample_0 + identifier: + - value: 01b01d59-07d3-481d-b466-bf77a916a0db + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-b3db0c02-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_74_sample_0_subject + identifier: + - value: GENIE-GRCC-b3db0c02-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f64a4a61-5d5c-49d3-8552-f3f5eb24e632 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_75_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_75_diagnosis_0 + identifier: + - value: 6ca9116f-412c-41d9-872b-1775f3d9464c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_75 + identifier: + - value: 0e609b0f-4db4-41c0-bf0b-f482f075cd71 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD11803 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25928 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_75_sample_0 + identifier: + - value: 3dac18fb-752c-42aa-bdad-9f91d54fb950 + system: http://crdc.nci.nih.gov/gdc + - value: AD11803_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_75_sample_0_subject + identifier: + - value: AD11803_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0e609b0f-4db4-41c0-bf0b-f482f075cd71 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_76_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_76_diagnosis_0 + identifier: + - value: 89e61c6e-3fb5-494b-81b3-7280119fefc9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_76 + identifier: + - value: 3d06d53b-3c3f-45e7-a0b9-cca26adbd387 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-011185 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_76_sample_0 + identifier: + - value: 25bebf87-88d5-4cd5-b2d7-3f2b7c1a0a02 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-011185-11116 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_76_sample_0_subject + identifier: + - value: GENIE-DFCI-011185-11116 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3d06d53b-3c3f-45e7-a0b9-cca26adbd387 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_77_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_77_diagnosis_0 + identifier: + - value: f7e49651-4dc5-50d9-af24-de743caf866b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_77 + identifier: + - value: 468649e7-1525-4b8a-8ab5-ddb27db5f022 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6482 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22741 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_77_sample_0 + identifier: + - value: 3a24aaeb-37ce-4508-81d5-e531aac8a167 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6482-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_77_sample_0_subject + identifier: + - value: TCGA-CR-6482-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 468649e7-1525-4b8a-8ab5-ddb27db5f022 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_77_sample_1 + identifier: + - value: 92173f97-b46a-4950-8cd8-6729ab9522c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6482-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_77_sample_1_subject + identifier: + - value: TCGA-CR-6482-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 468649e7-1525-4b8a-8ab5-ddb27db5f022 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_78_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_78_diagnosis_0 + identifier: + - value: e792cf88-dfe7-5130-ab9d-df59b3ed1b3b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_78 + identifier: + - value: e0acb3aa-4cb4-43c9-ae36-2213536666a6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7421 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27961 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1997-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_78_sample_0 + identifier: + - value: 40583cb5-46f0-4966-82c7-4149f14581d4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7421-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_78_sample_0_subject + identifier: + - value: TCGA-CV-7421-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e0acb3aa-4cb4-43c9-ae36-2213536666a6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_78_sample_1 + identifier: + - value: ef81caac-1fdd-43dd-80a3-4e18eb35271e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7421-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_78_sample_1_subject + identifier: + - value: TCGA-CV-7421-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e0acb3aa-4cb4-43c9-ae36-2213536666a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_78_sample_2 + identifier: + - value: 6766e43d-12fd-49ba-bdde-c19bb71d329d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7421-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_78_sample_2_subject + identifier: + - value: TCGA-CV-7421-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e0acb3aa-4cb4-43c9-ae36-2213536666a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_79_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_79_diagnosis_0 + identifier: + - value: 48994484-82cc-51ba-a8b6-6f4663599d40 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_79 + identifier: + - value: 467d5c94-1e67-4454-9e9c-9dffaa643032 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6478 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24244 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_79_sample_0 + identifier: + - value: a26d04d0-1501-4cc7-afea-154a89cff0ff + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6478-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_79_sample_0_subject + identifier: + - value: TCGA-CR-6478-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 467d5c94-1e67-4454-9e9c-9dffaa643032 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_79_sample_1 + identifier: + - value: dfbc5ddf-a361-4d72-ba8d-5615ca644357 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6478-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_79_sample_1_subject + identifier: + - value: TCGA-CR-6478-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 467d5c94-1e67-4454-9e9c-9dffaa643032 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_80_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_80_diagnosis_0 + identifier: + - value: a3c1a290-626e-5e1a-b120-0153a79fadd1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_80 + identifier: + - value: 277b02e9-ded5-4980-845d-af53690000ac + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4741 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27506 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_80_sample_0 + identifier: + - value: 03c9108a-5139-4bac-9641-c7dbbedef420 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4741-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_80_sample_0_subject + identifier: + - value: TCGA-CN-4741-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 277b02e9-ded5-4980-845d-af53690000ac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_80_sample_1 + identifier: + - value: a47974a3-b37e-4041-8953-5f50f8745681 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4741-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_80_sample_1_subject + identifier: + - value: TCGA-CN-4741-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 277b02e9-ded5-4980-845d-af53690000ac + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_80_sample_2 + identifier: + - value: 8d8ddca2-6461-4a8b-a696-da0906661b9e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4741-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_80_sample_2_subject + identifier: + - value: TCGA-CN-4741-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 277b02e9-ded5-4980-845d-af53690000ac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_81_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_81_diagnosis_0 + identifier: + - value: f6106a03-d94d-5b31-969b-ddd1d6ac23f7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_81 + identifier: + - value: 5646f226-e2ce-45ef-8aa2-4841ec6b56b0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-8596 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25408 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2005-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_81_sample_0 + identifier: + - value: 51eeba12-4cfb-4842-ad6c-e49cfe5ef207 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-8596-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_81_sample_0_subject + identifier: + - value: TCGA-BB-8596-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5646f226-e2ce-45ef-8aa2-4841ec6b56b0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_81_sample_1 + identifier: + - value: b8077f12-81e6-49f1-aa69-a4b6f5825534 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-8596-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_81_sample_1_subject + identifier: + - value: TCGA-BB-8596-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5646f226-e2ce-45ef-8aa2-4841ec6b56b0 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_81_sample_2 + identifier: + - value: 226992b4-f81f-49f5-a1da-37ab1742779b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-8596-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_81_sample_2_subject + identifier: + - value: TCGA-BB-8596-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5646f226-e2ce-45ef-8aa2-4841ec6b56b0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_82_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_82_diagnosis_0 + identifier: + - value: b0179bcd-bda0-42ff-8654-61f3fe576e73 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_82 + identifier: + - value: a0a330b8-734c-41ff-811f-a2caba7f1ffe + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD12050 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17686 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_82_sample_0 + identifier: + - value: 0a8dd963-c724-4a77-b662-5f711ac88607 + system: http://crdc.nci.nih.gov/gdc + - value: AD12050_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_82_sample_0_subject + identifier: + - value: AD12050_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a0a330b8-734c-41ff-811f-a2caba7f1ffe + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_83_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_83_diagnosis_0 + identifier: + - value: 65bd5ce4-bf44-4994-824e-f21701449f73 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_83 + identifier: + - value: 961b7a10-3499-40f4-8410-2fdac021afc0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-NKI-HMII + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_83_sample_0 + identifier: + - value: cb629447-dbb7-49c7-a88a-435b6b6decda + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-NKI-HMII-Q9EY + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_83_sample_0_subject + identifier: + - value: GENIE-NKI-HMII-Q9EY + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 961b7a10-3499-40f4-8410-2fdac021afc0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_84_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_84_diagnosis_0 + identifier: + - value: 82cf8f30-edc0-444a-9607-498f1f4fc6a5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_84 + identifier: + - value: 383611e8-122b-45b0-bd58-277b78ea5291 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-NKI-ETWO + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_84_sample_0 + identifier: + - value: 92e24628-56bc-4c65-9c4b-76c589943948 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-NKI-ETWO-SK3U + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_84_sample_0_subject + identifier: + - value: GENIE-NKI-ETWO-SK3U + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 383611e8-122b-45b0-bd58-277b78ea5291 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_85_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_85_diagnosis_0 + identifier: + - value: 5c70e571-fbe5-407f-aea2-9f740e6f5d2a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_85 + identifier: + - value: 794035f7-c253-4af1-b199-03e6faa0d89a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-002399 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_85_sample_0 + identifier: + - value: d57d8dd7-f0d5-4c3e-9ac7-cc23e2aa77d7 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-002399-7809 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_85_sample_0_subject + identifier: + - value: GENIE-DFCI-002399-7809 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 794035f7-c253-4af1-b199-03e6faa0d89a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_86_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_86_diagnosis_0 + identifier: + - value: 26a2438a-f914-4865-9784-a9a47150cb4e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_86 + identifier: + - value: e5b0504e-32a4-4032-a4c8-b99d13808e75 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010260 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_86_sample_0 + identifier: + - value: 0d696183-2cc4-4f33-9973-04537cb86276 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010260-9348 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_86_sample_0_subject + identifier: + - value: GENIE-DFCI-010260-9348 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e5b0504e-32a4-4032-a4c8-b99d13808e75 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_87_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_87_diagnosis_0 + identifier: + - value: 04081703-b701-4765-8309-0a204a48c183 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_87 + identifier: + - value: e89f8714-4c48-4987-a70b-4ec8bf0f9296 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-201710 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_87_sample_0 + identifier: + - value: cc51bca3-858a-4ac3-b48a-c4d273b2329c + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-201710-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_87_sample_0_subject + identifier: + - value: GENIE-VICC-201710-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e89f8714-4c48-4987-a70b-4ec8bf0f9296 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_88_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_88_diagnosis_0 + identifier: + - value: 64017f79-8293-4fd3-8af0-bf01eb6cf49c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_88 + identifier: + - value: 354798d8-d883-402f-82ee-238bb83827bc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-UHN-653571 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_88_sample_0 + identifier: + - value: 5349f1ac-ad8d-437f-a9e7-30b2323bd11f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-UHN-653571-ARC1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_88_sample_0_subject + identifier: + - value: GENIE-UHN-653571-ARC1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 354798d8-d883-402f-82ee-238bb83827bc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_89_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_89_diagnosis_0 + identifier: + - value: 08272717-6b2b-4734-9674-4bec2662bd32 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_89 + identifier: + - value: ccd1015f-0dab-45c5-b957-cb69accd7355 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-UHN-523097 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_89_sample_0 + identifier: + - value: ffef8dac-d99c-4426-ad9e-f4e3947fe1c1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-UHN-523097-ARC1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_89_sample_0_subject + identifier: + - value: GENIE-UHN-523097-ARC1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ccd1015f-0dab-45c5-b957-cb69accd7355 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_90_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_90_diagnosis_0 + identifier: + - value: 96e73819-3b05-4a68-90bb-ceb60d419d50 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_90 + identifier: + - value: 0a277de5-365f-4fe6-9513-199a387cb4d0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006296 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_90_sample_0 + identifier: + - value: 51ca54fe-f436-4a88-a11d-ab0781666edf + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006296-6704 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_90_sample_0_subject + identifier: + - value: GENIE-DFCI-006296-6704 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0a277de5-365f-4fe6-9513-199a387cb4d0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_91_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_91_diagnosis_0 + identifier: + - value: ca8f5806-a2af-45ee-8217-e6dfc4d0b229 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_91 + identifier: + - value: 14773fa6-32ed-4075-893e-72d3e13a844f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0012391 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_91_sample_0 + identifier: + - value: 3c8fe733-1711-4d4a-a64c-b94788eda279 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0012391-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_91_sample_0_subject + identifier: + - value: GENIE-MSK-P-0012391-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 14773fa6-32ed-4075-893e-72d3e13a844f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_92_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_92_diagnosis_0 + identifier: + - value: 155ca101-ad45-4f50-b9ac-45908daffab8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_92 + identifier: + - value: d412bdae-6b9f-49ee-8d42-f6269bcf4a49 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003009 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_92_sample_0 + identifier: + - value: f8de95dc-1011-4b86-9a46-28bc46465195 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003009-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_92_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003009-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d412bdae-6b9f-49ee-8d42-f6269bcf4a49 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_93_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_93_diagnosis_0 + identifier: + - value: cde79cd2-3aab-48ed-81a1-259a3cd21002 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_93 + identifier: + - value: 56de8cee-06fb-4313-a767-fa3cdf3bd74e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-122614 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_93_sample_0 + identifier: + - value: 71ba3119-c343-43f0-84db-4ba8787d316b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-122614-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_93_sample_0_subject + identifier: + - value: GENIE-VICC-122614-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 56de8cee-06fb-4313-a767-fa3cdf3bd74e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_94_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_94_diagnosis_0 + identifier: + - value: d284c064-ed2c-5741-b1ad-2f9fd34b6636 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_94 + identifier: + - value: b3631718-9e0a-454c-bee1-8f36ebc509d8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-5153 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18743 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2005-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_94_sample_0 + identifier: + - value: f079e825-160a-40d5-97cc-1931f11c4e2e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5153-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_94_sample_0_subject + identifier: + - value: TCGA-BA-5153-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b3631718-9e0a-454c-bee1-8f36ebc509d8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_94_sample_1 + identifier: + - value: 2f668e36-b359-488e-b0fc-fb7bb479f485 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5153-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_94_sample_1_subject + identifier: + - value: TCGA-BA-5153-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b3631718-9e0a-454c-bee1-8f36ebc509d8 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_94_sample_2 + identifier: + - value: 2dc7070a-9c70-4bb1-9634-8c934bb9c8d1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5153-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_94_sample_2_subject + identifier: + - value: TCGA-BA-5153-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b3631718-9e0a-454c-bee1-8f36ebc509d8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_95_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_95_diagnosis_0 + identifier: + - value: 52d5ae11-4bb0-53aa-bff7-31190888f8ff + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_95 + identifier: + - value: 692b50fc-19ca-4926-84cb-fd7168209e44 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-5247 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17810 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_95_sample_0 + identifier: + - value: 950233c0-c1ca-4b69-8e3f-a6072dbc7e6a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5247-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_95_sample_0_subject + identifier: + - value: TCGA-CR-5247-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 692b50fc-19ca-4926-84cb-fd7168209e44 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_95_sample_1 + identifier: + - value: 43739161-8083-4740-a670-1a334a87ca7e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5247-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_95_sample_1_subject + identifier: + - value: TCGA-CR-5247-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 692b50fc-19ca-4926-84cb-fd7168209e44 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_96_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_96_diagnosis_0 + identifier: + - value: 1ddea2fe-7874-5d31-b1fe-2cb2b0de542f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_96 + identifier: + - value: abbcc1d8-ab74-4459-bf28-cc627bef440e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-KU-A6H7 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20314 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_96_sample_0 + identifier: + - value: b4074f91-5478-4117-bee5-ed164e4d38c2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A6H7-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_96_sample_0_subject + identifier: + - value: TCGA-KU-A6H7-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: abbcc1d8-ab74-4459-bf28-cc627bef440e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 36 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_96_sample_1 + identifier: + - value: 840d3da5-0493-460a-b5a9-4285e1a2ad37 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A6H7-06A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_96_sample_1_subject + identifier: + - value: TCGA-KU-A6H7-06A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: abbcc1d8-ab74-4459-bf28-cc627bef440e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 36 + unit: + coding: *id001 + quantity_collected: + value_decimal: 670 + unit: + coding: &id002 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_96_sample_2 + identifier: + - value: 61eec5b6-925d-434b-a318-b22fc21c9ffe + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A6H7-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_96_sample_2_subject + identifier: + - value: TCGA-KU-A6H7-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: abbcc1d8-ab74-4459-bf28-cc627bef440e + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_96_sample_3 + identifier: + - value: e4439379-d930-4b9a-b498-3b75e569f8ad + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A6H7-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_96_sample_3_subject + identifier: + - value: TCGA-KU-A6H7-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: abbcc1d8-ab74-4459-bf28-cc627bef440e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 36 + unit: + coding: *id001 + quantity_collected: + value_decimal: 80 + unit: + coding: *id002 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_97_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_97_diagnosis_0 + identifier: + - value: 9d69f6a3-4edb-54e3-a840-ff1ff0aefb30 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_97 + identifier: + - value: 1ca54115-93a3-4c0e-abf0-915b4bbff10c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A7JK + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21696 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_97_sample_0 + identifier: + - value: 15776f80-0722-45a8-bc97-cc209cef631b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JK-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_97_sample_0_subject + identifier: + - value: TCGA-UF-A7JK-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1ca54115-93a3-4c0e-abf0-915b4bbff10c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1302 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_97_sample_1 + identifier: + - value: 56c76698-7155-4f7a-9f9e-4fb62c673599 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JK-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_97_sample_1_subject + identifier: + - value: TCGA-UF-A7JK-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1ca54115-93a3-4c0e-abf0-915b4bbff10c + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_97_sample_2 + identifier: + - value: 90e4a976-0d97-47ef-aa29-295c2afeb31b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JK-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_97_sample_2_subject + identifier: + - value: TCGA-UF-A7JK-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1ca54115-93a3-4c0e-abf0-915b4bbff10c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1302 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_98_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_98_diagnosis_0 + identifier: + - value: f29e70db-e331-5bcb-82fc-f2e15cad5985 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_98 + identifier: + - value: c9c33b2a-bf99-4563-a220-01a5dbe3be92 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7433 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18004 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_98_sample_0 + identifier: + - value: c2530f39-c334-4a38-b75b-b74d5cb95920 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7433-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_98_sample_0_subject + identifier: + - value: TCGA-CV-7433-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c9c33b2a-bf99-4563-a220-01a5dbe3be92 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_98_sample_1 + identifier: + - value: 5c4960e6-92f7-4576-a7d8-82a7c3d7cd5f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7433-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_98_sample_1_subject + identifier: + - value: TCGA-CV-7433-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c9c33b2a-bf99-4563-a220-01a5dbe3be92 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_98_sample_2 + identifier: + - value: 2916fc1e-ba62-4494-8014-dfcc6dd358ea + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7433-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_98_sample_2_subject + identifier: + - value: TCGA-CV-7433-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c9c33b2a-bf99-4563-a220-01a5dbe3be92 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_99_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_99_diagnosis_0 + identifier: + - value: 4bcd5e25-adf6-5fe2-b07f-05d72b7b22a1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_99 + identifier: + - value: 91d44093-d8d9-442c-92ed-e659c45b4e0a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A6T6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19694 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.1 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_99_sample_0 + identifier: + - value: 3147ba3d-b1fd-4e40-82e1-56429f2389d6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6T6-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_99_sample_0_subject + identifier: + - value: TCGA-P3-A6T6-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 91d44093-d8d9-442c-92ed-e659c45b4e0a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_99_sample_1 + identifier: + - value: 6f0b02c4-6efb-4104-89e1-2e76811b6afc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6T6-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_99_sample_1_subject + identifier: + - value: TCGA-P3-A6T6-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 91d44093-d8d9-442c-92ed-e659c45b4e0a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1333 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_99_sample_2 + identifier: + - value: 127b2222-93b1-4870-93f2-867d8e69d015 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6T6-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_99_sample_2_subject + identifier: + - value: TCGA-P3-A6T6-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 91d44093-d8d9-442c-92ed-e659c45b4e0a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1333 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_100_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_100_diagnosis_0 + identifier: + - value: 7c7482aa-6349-58c9-ab17-6c69acbd579e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_100 + identifier: + - value: 511b1de1-b855-47bb-a2f8-58dc5792be47 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7388 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25728 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_100_sample_0 + identifier: + - value: c6aafc51-6295-494f-9bf2-1e4f43a72ae0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7388-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_100_sample_0_subject + identifier: + - value: TCGA-CR-7388-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 511b1de1-b855-47bb-a2f8-58dc5792be47 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_100_sample_1 + identifier: + - value: f27e3255-bc73-4943-8201-5245b85c4ee5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7388-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_100_sample_1_subject + identifier: + - value: TCGA-CR-7388-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 511b1de1-b855-47bb-a2f8-58dc5792be47 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_101_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_101_diagnosis_0 + identifier: + - value: c18fbc5a-880d-5f56-8466-527763c437d6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_101 + identifier: + - value: e7174299-3ca7-4d51-9048-3ef3efde4e5c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A45Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27397 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 5th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_101_sample_0 + identifier: + - value: fc3d6178-acc8-4e4f-b935-3cc1f6c0f304 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45Z-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_101_sample_0_subject + identifier: + - value: TCGA-CV-A45Z-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e7174299-3ca7-4d51-9048-3ef3efde4e5c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4438 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_101_sample_1 + identifier: + - value: 866bc103-c5bc-4365-8ef6-40064b33046d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45Z-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_101_sample_1_subject + identifier: + - value: TCGA-CV-A45Z-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e7174299-3ca7-4d51-9048-3ef3efde4e5c + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_101_sample_2 + identifier: + - value: f844574a-cb7f-4f66-83d4-ee0ca41a63d1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45Z-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_101_sample_2_subject + identifier: + - value: TCGA-CV-A45Z-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e7174299-3ca7-4d51-9048-3ef3efde4e5c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4438 + unit: + coding: *id001 + quantity_collected: + value_decimal: 160 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_102_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_102_diagnosis_0 + identifier: + - value: fac833bd-36d8-5306-b322-92106575bfe1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_102 + identifier: + - value: a4fcb7fd-9c22-4486-99c5-97da050c9fb3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5430 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22577 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_102_sample_0 + identifier: + - value: 72f98dc0-3fcb-47a4-8c7a-52a7cd9d3fdf + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5430-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_102_sample_0_subject + identifier: + - value: TCGA-CV-5430-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4fcb7fd-9c22-4486-99c5-97da050c9fb3 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_102_sample_1 + identifier: + - value: 4151c76f-9dcb-4451-a99b-889e0024f8b9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5430-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_102_sample_1_subject + identifier: + - value: TCGA-CV-5430-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4fcb7fd-9c22-4486-99c5-97da050c9fb3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_102_sample_2 + identifier: + - value: 5d293d68-61ae-49ad-bfcc-e0bdb91cc29e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5430-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_102_sample_2_subject + identifier: + - value: TCGA-CV-5430-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4fcb7fd-9c22-4486-99c5-97da050c9fb3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_102_sample_3 + identifier: + - value: 5bae7161-8838-4b10-9210-02deaae4b9c1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5430-11B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_102_sample_3_subject + identifier: + - value: TCGA-CV-5430-11B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4fcb7fd-9c22-4486-99c5-97da050c9fb3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_103_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_103_diagnosis_0 + identifier: + - value: 022d6f9b-38da-5bfb-8bd9-e800361481a0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_103 + identifier: + - value: f248d7b9-6ea7-44ef-8af6-8beda6c6ba4a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-A6EK + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24558 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_103_sample_0 + identifier: + - value: ad47c17b-e21c-4aed-aac6-8a062c6b5e42 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EK-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_103_sample_0_subject + identifier: + - value: TCGA-D6-A6EK-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f248d7b9-6ea7-44ef-8af6-8beda6c6ba4a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 211 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_103_sample_1 + identifier: + - value: 0a64b28d-8dde-4eaf-bac5-217406cbc4c6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EK-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_103_sample_1_subject + identifier: + - value: TCGA-D6-A6EK-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f248d7b9-6ea7-44ef-8af6-8beda6c6ba4a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 211 + unit: + coding: *id001 + quantity_collected: + value_decimal: 130 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_103_sample_2 + identifier: + - value: b3a55bcd-1f88-4d25-9f95-5ef7393d6cf0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EK-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_103_sample_2_subject + identifier: + - value: TCGA-D6-A6EK-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f248d7b9-6ea7-44ef-8af6-8beda6c6ba4a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_104_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_104_diagnosis_0 + identifier: + - value: 11688639-0783-576d-ac58-40e8e3a19be6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_104 + identifier: + - value: b39d2880-6964-4c5b-b5a9-ab64e5cb31e8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A49C + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24495 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_104_sample_0 + identifier: + - value: 7758f04c-0e07-4e8a-882d-ece76469f433 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A49C-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_104_sample_0_subject + identifier: + - value: TCGA-CN-A49C-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b39d2880-6964-4c5b-b5a9-ab64e5cb31e8 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 132 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_104_sample_1 + identifier: + - value: 34b36112-f260-4bf4-90b7-0cebc5988b59 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A49C-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_104_sample_1_subject + identifier: + - value: TCGA-CN-A49C-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b39d2880-6964-4c5b-b5a9-ab64e5cb31e8 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 85 + unit: + coding: *id001 + quantity_collected: + value_decimal: 230 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_105_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_105_diagnosis_0 + identifier: + - value: af8fdb73-f4a3-5b32-b9d5-6f9d39a97856 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_105 + identifier: + - value: 63f6a127-e4e8-4e1c-8236-a2adb9594c8f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-6824 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22633 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_105_sample_0 + identifier: + - value: 2e1366b9-95b7-4a0d-81f0-7ec14e4f4592 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6824-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_105_sample_0_subject + identifier: + - value: TCGA-D6-6824-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 63f6a127-e4e8-4e1c-8236-a2adb9594c8f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_105_sample_1 + identifier: + - value: 10c45c93-36f6-4085-8bc8-f46dfdedca1f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6824-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_105_sample_1_subject + identifier: + - value: TCGA-D6-6824-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 63f6a127-e4e8-4e1c-8236-a2adb9594c8f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_105_sample_2 + identifier: + - value: 4d8bbfbd-1a39-4630-a1e5-3bc6abb01949 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6824-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_105_sample_2_subject + identifier: + - value: TCGA-D6-6824-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 63f6a127-e4e8-4e1c-8236-a2adb9594c8f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_106_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_106_diagnosis_0 + identifier: + - value: 53ddd4d3-8e0e-4e6f-9cd1-fe6c9c5eb114 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_106 + identifier: + - value: 4b6fa057-5bb4-4ee5-a119-758ac208920f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0006525 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_106_sample_0 + identifier: + - value: 379984ec-2e8f-4c3e-9153-1ec8adc17770 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0006525-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_106_sample_0_subject + identifier: + - value: GENIE-MSK-P-0006525-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b6fa057-5bb4-4ee5-a119-758ac208920f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_107_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_107_diagnosis_0 + identifier: + - value: de3c2719-988d-4266-98cd-c1139a2cc412 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_107 + identifier: + - value: 5aea1976-94d2-46da-baf5-a198774cc237 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0006641 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_107_sample_0 + identifier: + - value: 4e6ffe6c-feee-4dca-b56d-0f2c8b498ae6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0006641-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_107_sample_0_subject + identifier: + - value: GENIE-MSK-P-0006641-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5aea1976-94d2-46da-baf5-a198774cc237 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_108_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_108_diagnosis_0 + identifier: + - value: f14b2d60-39ff-428e-bfb9-a33f4d3242ee + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_108 + identifier: + - value: 4bae7638-f9e8-4d8f-a4a5-305e3d32e790 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002193 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_108_sample_0 + identifier: + - value: f2f48558-d331-431f-a14d-845efe0c6ce9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002193-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_108_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002193-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4bae7638-f9e8-4d8f-a4a5-305e3d32e790 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_109_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_109_diagnosis_0 + identifier: + - value: 0c55f80d-c82c-4554-916f-6b117978b3fc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_109 + identifier: + - value: bd792bb2-f639-45f4-bd78-a81876cf6a94 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000454 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_109_sample_0 + identifier: + - value: 5c3a5e81-481c-430b-9c70-f2d61a77568d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000454-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_109_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000454-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: bd792bb2-f639-45f4-bd78-a81876cf6a94 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_110_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_110_diagnosis_0 + identifier: + - value: c652d5fb-652f-485c-99cd-4e3e00af1126 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_110 + identifier: + - value: 09f69d33-beac-4a07-9df9-39ea007562ce + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000396 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_110_sample_0 + identifier: + - value: 2bde1811-da29-46e9-973a-45ea43387818 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000396-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_110_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000396-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 09f69d33-beac-4a07-9df9-39ea007562ce + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_111_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_111_diagnosis_0 + identifier: + - value: 4ac21d4b-c592-4afd-bfc1-278702612bd6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_111 + identifier: + - value: 503663e7-5e26-4124-a1cb-2be0a0ca8846 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004838 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_111_sample_0 + identifier: + - value: 10d245b5-b16d-40ee-bd41-bd08a0355894 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004838-2080 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_111_sample_0_subject + identifier: + - value: GENIE-DFCI-004838-2080 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 503663e7-5e26-4124-a1cb-2be0a0ca8846 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_112_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_112_diagnosis_0 + identifier: + - value: 00ed54be-bd0c-5950-9165-b08535ef9f18 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_112 + identifier: + - value: 896f5dcc-d076-4e1f-ae7c-52d21109da7b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-TN-A7HI + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20666 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_112_sample_0 + identifier: + - value: 3ad15aca-9197-4512-8bb9-77099ae8f049 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HI-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_112_sample_0_subject + identifier: + - value: TCGA-TN-A7HI-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 896f5dcc-d076-4e1f-ae7c-52d21109da7b + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_112_sample_1 + identifier: + - value: 2a081426-e4fe-4868-adc9-c14142490b81 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HI-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_112_sample_1_subject + identifier: + - value: TCGA-TN-A7HI-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 896f5dcc-d076-4e1f-ae7c-52d21109da7b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 75 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_112_sample_2 + identifier: + - value: 9808b586-4541-42a8-a72c-0c043ff568b3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HI-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_112_sample_2_subject + identifier: + - value: TCGA-TN-A7HI-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 896f5dcc-d076-4e1f-ae7c-52d21109da7b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 75 + unit: + coding: *id001 + quantity_collected: + value_decimal: 140 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_113_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_113_diagnosis_0 + identifier: + - value: 1f6860df-38fb-5519-8ec9-3068b0476cf2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_113 + identifier: + - value: fe844945-3ea9-449e-993c-df392fabcfd0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4735 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19107 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_113_sample_0 + identifier: + - value: a2caeab5-55a4-412f-a647-0112f48bbbe7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4735-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_113_sample_0_subject + identifier: + - value: TCGA-CN-4735-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fe844945-3ea9-449e-993c-df392fabcfd0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_113_sample_1 + identifier: + - value: feb21d9d-394f-402d-8659-eb15bb95f0db + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4735-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_113_sample_1_subject + identifier: + - value: TCGA-CN-4735-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fe844945-3ea9-449e-993c-df392fabcfd0 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_113_sample_2 + identifier: + - value: fbb300fa-8793-42da-a68e-4570ae2e5186 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4735-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_113_sample_2_subject + identifier: + - value: TCGA-CN-4735-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fe844945-3ea9-449e-993c-df392fabcfd0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_114_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_114_diagnosis_0 + identifier: + - value: 8723983c-94ff-55df-8165-6fd5937b5462 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_114 + identifier: + - value: a3f98e70-7050-46cf-a679-ca7a83f4442f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A63T + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22201 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_114_sample_0 + identifier: + - value: 75c0a7b6-3e82-4ce9-8856-dd3475affe87 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63T-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_114_sample_0_subject + identifier: + - value: TCGA-CN-A63T-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a3f98e70-7050-46cf-a679-ca7a83f4442f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_114_sample_1 + identifier: + - value: b477dfb8-c039-49d5-9a0e-912946dc3ad1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63T-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_114_sample_1_subject + identifier: + - value: TCGA-CN-A63T-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a3f98e70-7050-46cf-a679-ca7a83f4442f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 519 + unit: + coding: *id001 + quantity_collected: + value_decimal: 150 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_114_sample_2 + identifier: + - value: 74606f8c-46a7-453e-acfd-91203aec6df7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63T-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_114_sample_2_subject + identifier: + - value: TCGA-CN-A63T-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a3f98e70-7050-46cf-a679-ca7a83f4442f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 519 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_115_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_115_diagnosis_0 + identifier: + - value: ea4330da-9d29-4e64-8197-55a50ee283dd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_115 + identifier: + - value: 4ccad595-5894-439a-833a-29e424ba9f37 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001557 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_115_sample_0 + identifier: + - value: 90c9d5f2-ca54-4084-99e7-e9407e364b12 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001557-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_115_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001557-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4ccad595-5894-439a-833a-29e424ba9f37 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_116_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_116_diagnosis_0 + identifier: + - value: 530535a6-b47e-48ce-b312-54c3003c14ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_116 + identifier: + - value: decb1f2c-9899-4479-931c-bfa2d645f922 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002854 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_116_sample_0 + identifier: + - value: ad472d22-bccd-401b-ab2d-0ab7a31c7b73 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002854-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_116_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002854-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: decb1f2c-9899-4479-931c-bfa2d645f922 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_117_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_117_diagnosis_0 + identifier: + - value: 748313dd-50be-45e2-9d94-75752dd6e783 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_117 + identifier: + - value: 8405bfba-60fc-4f71-ac09-7b822f6d74d2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD10965 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21784 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_117_sample_0 + identifier: + - value: 97354824-7fe1-472e-ac48-74ad10e5da51 + system: http://crdc.nci.nih.gov/gdc + - value: AD10965_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_117_sample_0_subject + identifier: + - value: AD10965_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8405bfba-60fc-4f71-ac09-7b822f6d74d2 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_118_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_118_diagnosis_0 + identifier: + - value: e7406302-5dd6-45b1-ae98-a8094c495943 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_118 + identifier: + - value: 14b0ede8-75f6-47ff-b489-cd5435276f66 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD13780 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 30718 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_118_sample_0 + identifier: + - value: c9bccdb4-1bd0-44e0-bfb0-7588611ab01b + system: http://crdc.nci.nih.gov/gdc + - value: AD13780_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_118_sample_0_subject + identifier: + - value: AD13780_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 14b0ede8-75f6-47ff-b489-cd5435276f66 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_119_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_119_diagnosis_0 + identifier: + - value: 4a315682-7cd0-4c42-9fd0-50ec841a059f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_119 + identifier: + - value: 676f0a41-ced0-4b61-96ab-9665f7cc2775 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004723 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_119_sample_0 + identifier: + - value: 1291884d-38d8-49cf-b16e-aeab69d83681 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004723-1663 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_119_sample_0_subject + identifier: + - value: GENIE-DFCI-004723-1663 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 676f0a41-ced0-4b61-96ab-9665f7cc2775 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_120_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_120_diagnosis_0 + identifier: + - value: 27fbdde4-c58a-46d7-a96f-918b64fe5b51 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_120 + identifier: + - value: a2c0b0a4-cc1c-4372-9184-5d994a49eb26 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037700 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_120_sample_0 + identifier: + - value: 50b8e07c-b892-4fac-bf59-9e093e2d74d3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037700-159036 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_120_sample_0_subject + identifier: + - value: GENIE-DFCI-037700-159036 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a2c0b0a4-cc1c-4372-9184-5d994a49eb26 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_121_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_121_diagnosis_0 + identifier: + - value: 12d5265d-8eb5-4122-9e4d-976bdc0ded08 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_121 + identifier: + - value: a8b97361-50ad-465b-b405-82996c650fe0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002469 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_121_sample_0 + identifier: + - value: ed3acbbc-fb24-4be6-b09c-e0b6f4d9814f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002469-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_121_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002469-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a8b97361-50ad-465b-b405-82996c650fe0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_122_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_122_diagnosis_0 + identifier: + - value: 6b3df15b-f5c6-4c79-923c-572688a90a50 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_122 + identifier: + - value: 1ba151a5-45a8-4b82-8127-89c5bf2928cb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD1220 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 9410 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_122_sample_0 + identifier: + - value: 2bbdf4c4-88a1-4358-a88a-5daa2a9a506d + system: http://crdc.nci.nih.gov/gdc + - value: AD1220_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_122_sample_0_subject + identifier: + - value: AD1220_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1ba151a5-45a8-4b82-8127-89c5bf2928cb + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_123_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_123_diagnosis_0 + identifier: + - value: 85d63c6e-a6c1-47a5-92a9-216719073a4a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_123 + identifier: + - value: d7c7ecbd-7495-4d29-8bb6-78797f5a47eb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004072 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_123_sample_0 + identifier: + - value: 9a26d9df-9ab2-48df-ada8-8bd8455cccd6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004072-413 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_123_sample_0_subject + identifier: + - value: GENIE-DFCI-004072-413 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d7c7ecbd-7495-4d29-8bb6-78797f5a47eb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_124_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_124_diagnosis_0 + identifier: + - value: 100193fa-11a9-4abd-9bcb-b1688eefaf5e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_124 + identifier: + - value: 3509a239-54eb-4d6e-92c8-267dc8a21b04 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008981 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_124_sample_0 + identifier: + - value: 8fe03287-0b1e-4750-9006-58059562a243 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008981-6260 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_124_sample_0_subject + identifier: + - value: GENIE-DFCI-008981-6260 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3509a239-54eb-4d6e-92c8-267dc8a21b04 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_125_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_125_diagnosis_0 + identifier: + - value: 3c0d1fbc-508c-4cad-a9eb-a848fc20ac76 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_125 + identifier: + - value: 05e144e8-5936-4026-b71b-47b5cd8c9514 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006868 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_125_sample_0 + identifier: + - value: abf5cf5e-2352-4ba7-9a91-cbefe78ae28e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006868-2957 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_125_sample_0_subject + identifier: + - value: GENIE-DFCI-006868-2957 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 05e144e8-5936-4026-b71b-47b5cd8c9514 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_126_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_126_diagnosis_0 + identifier: + - value: 3cb5d51d-2566-4b1f-ad4f-57520007e73d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_126 + identifier: + - value: 5c6fed46-2708-47fe-9034-49f196657648 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-050743 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_126_sample_0 + identifier: + - value: c862481b-aaaf-41d4-9c29-188760a43dd8 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-050743-203353 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_126_sample_0_subject + identifier: + - value: GENIE-DFCI-050743-203353 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5c6fed46-2708-47fe-9034-49f196657648 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_127_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_127_diagnosis_0 + identifier: + - value: f9e5f978-310f-4011-86bd-f468da998bd3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_127 + identifier: + - value: 0c5a0773-3cd7-4e8a-b54c-c2b3bb7f612e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015030 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_127_sample_0 + identifier: + - value: e3362d03-8d6c-4be0-b1a6-5ce9c230f4f0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015030-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_127_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015030-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0c5a0773-3cd7-4e8a-b54c-c2b3bb7f612e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_128_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_128_diagnosis_0 + identifier: + - value: 5976f296-bcb7-49a6-8db6-8620875f12e3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_128 + identifier: + - value: 5ba6ada4-f93e-4309-bb14-0117d5ffe6a2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008036 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_128_sample_0 + identifier: + - value: 257963cb-44bc-4946-ac72-7a1bb02f6af9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008036-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_128_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008036-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ba6ada4-f93e-4309-bb14-0117d5ffe6a2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_129_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_129_diagnosis_0 + identifier: + - value: af2c06c6-b5cb-4369-906f-727e8e00e459 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_129 + identifier: + - value: edf4d925-3841-48cb-aeb1-c5b96fd39047 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005169 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_129_sample_0 + identifier: + - value: 104530ac-b606-41bc-93e4-5734f176d3bb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005169-1136 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_129_sample_0_subject + identifier: + - value: GENIE-DFCI-005169-1136 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: edf4d925-3841-48cb-aeb1-c5b96fd39047 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_130_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_130_diagnosis_0 + identifier: + - value: c0bf8ccd-6f3b-5ede-b3ce-a63ad584ab1b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_130 + identifier: + - value: f6ebe511-a4df-4310-bd59-3a46d43f100b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-DQ-7595 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19530 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_130_sample_0 + identifier: + - value: 52e0aaf1-d93b-42f8-b0e3-f6b4a3d0bd1e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7595-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_130_sample_0_subject + identifier: + - value: TCGA-DQ-7595-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f6ebe511-a4df-4310-bd59-3a46d43f100b + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_130_sample_1 + identifier: + - value: c522234a-c0b1-427a-8992-84fcfc9389ef + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7595-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_130_sample_1_subject + identifier: + - value: TCGA-DQ-7595-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f6ebe511-a4df-4310-bd59-3a46d43f100b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_130_sample_2 + identifier: + - value: 387e8df2-f053-4cbe-aae8-5727d215f904 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7595-10D + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_130_sample_2_subject + identifier: + - value: TCGA-DQ-7595-10D + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f6ebe511-a4df-4310-bd59-3a46d43f100b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 499 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_131_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_131_diagnosis_0 + identifier: + - value: 9e30aa6c-91e6-5dd3-9512-75c162a89913 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_131 + identifier: + - value: ac511727-185b-4ac0-b6c0-dc3a79657be6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A8Z8 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22107 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_131_sample_0 + identifier: + - value: a118da56-784d-4b67-aade-d9a7a8b49f18 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8Z8-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_131_sample_0_subject + identifier: + - value: TCGA-QK-A8Z8-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ac511727-185b-4ac0-b6c0-dc3a79657be6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 50 + unit: + coding: *id001 + quantity_collected: + value_decimal: 80 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_131_sample_1 + identifier: + - value: cff6967e-e8f7-4a25-aa31-9328e4b42816 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8Z8-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_131_sample_1_subject + identifier: + - value: TCGA-QK-A8Z8-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ac511727-185b-4ac0-b6c0-dc3a79657be6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_131_sample_2 + identifier: + - value: 1efb2d28-ac51-4d70-a24d-667a2b53467a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8Z8-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_131_sample_2_subject + identifier: + - value: TCGA-QK-A8Z8-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ac511727-185b-4ac0-b6c0-dc3a79657be6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 50 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_132_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_132_diagnosis_0 + identifier: + - value: a66ce9f9-d7d0-5f2e-b0c0-73f306f68236 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_132 + identifier: + - value: fafd6f5b-1d76-4537-bd1c-e0bd7b4e2166 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-6869 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22765 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_132_sample_0 + identifier: + - value: f4ed2c84-39f8-4ab3-8762-a9920acc2432 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6869-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_132_sample_0_subject + identifier: + - value: TCGA-BA-6869-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fafd6f5b-1d76-4537-bd1c-e0bd7b4e2166 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_132_sample_1 + identifier: + - value: 0aaa8bba-f4a5-4158-b9b4-a02244b5f6f7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6869-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_132_sample_1_subject + identifier: + - value: TCGA-BA-6869-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fafd6f5b-1d76-4537-bd1c-e0bd7b4e2166 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_132_sample_2 + identifier: + - value: 2f9729e6-edea-4612-82b3-01251317074a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6869-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_132_sample_2_subject + identifier: + - value: TCGA-BA-6869-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fafd6f5b-1d76-4537-bd1c-e0bd7b4e2166 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_133_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_133_diagnosis_0 + identifier: + - value: ac0363ed-feba-5584-802a-a8bd096fb07c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_133 + identifier: + - value: 339f80f9-a542-4aaa-8bb8-3784493dd5ab + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6022 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17971 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_133_sample_0 + identifier: + - value: d452d59e-92ff-46ee-840d-df8a161ca9c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6022-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_133_sample_0_subject + identifier: + - value: TCGA-CN-6022-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 339f80f9-a542-4aaa-8bb8-3784493dd5ab + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_133_sample_1 + identifier: + - value: 3b8fd8fb-429a-47ac-8b99-ae42a3fe968d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6022-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_133_sample_1_subject + identifier: + - value: TCGA-CN-6022-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 339f80f9-a542-4aaa-8bb8-3784493dd5ab + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_133_sample_2 + identifier: + - value: 952f71e6-b64c-456d-8d00-45e4118fef96 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6022-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_133_sample_2_subject + identifier: + - value: TCGA-CN-6022-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 339f80f9-a542-4aaa-8bb8-3784493dd5ab + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_134_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_134_diagnosis_0 + identifier: + - value: 18d9c548-2f10-5116-bf59-05cc53b3b5c6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_134 + identifier: + - value: 06f0cf45-3840-44b2-bfc5-18eb980b8f68 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7410 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22302 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1993-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_134_sample_0 + identifier: + - value: acd6cfc3-412b-4f61-a2c7-013c61fa2efe + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7410-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_134_sample_0_subject + identifier: + - value: TCGA-CV-7410-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 06f0cf45-3840-44b2-bfc5-18eb980b8f68 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_134_sample_1 + identifier: + - value: a24e0ad7-668e-4bc7-ae3a-94964278a407 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7410-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_134_sample_1_subject + identifier: + - value: TCGA-CV-7410-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 06f0cf45-3840-44b2-bfc5-18eb980b8f68 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_134_sample_2 + identifier: + - value: 843ced6e-a9be-48ea-9313-13aa752dbbe1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7410-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_134_sample_2_subject + identifier: + - value: TCGA-CV-7410-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 06f0cf45-3840-44b2-bfc5-18eb980b8f68 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_135_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_135_diagnosis_0 + identifier: + - value: f0cdd17d-5db9-4c58-84f5-f9efcc94dcb5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_135 + identifier: + - value: b8456353-3d86-4a2c-8e64-f67687761d61 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0004492 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_135_sample_0 + identifier: + - value: d74d27e4-88e8-4ce3-a1ff-7658e007a49a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0004492-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_135_sample_0_subject + identifier: + - value: GENIE-MSK-P-0004492-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b8456353-3d86-4a2c-8e64-f67687761d61 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_136_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_136_diagnosis_0 + identifier: + - value: a6576ff2-b9cf-40dd-8da4-ca829d762cc0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_136 + identifier: + - value: 71f27aa8-81cf-4d09-9d59-2b485b4ae237 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-001449 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_136_sample_0 + identifier: + - value: 4ec8fe70-22ad-4f62-893d-f95d77dd37f5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-001449-6594 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_136_sample_0_subject + identifier: + - value: GENIE-DFCI-001449-6594 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 71f27aa8-81cf-4d09-9d59-2b485b4ae237 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_137_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_137_diagnosis_0 + identifier: + - value: 9223ac2b-219b-423b-bd4f-5d28e84c8d89 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_137 + identifier: + - value: 975dff45-8236-4bd7-b985-a3ae6e4ad587 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-001409 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_137_sample_0 + identifier: + - value: fc3b12ce-4c74-4faa-ad8b-60ddde831901 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-001409-5066 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_137_sample_0_subject + identifier: + - value: GENIE-DFCI-001409-5066 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 975dff45-8236-4bd7-b985-a3ae6e4ad587 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_138_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_138_diagnosis_0 + identifier: + - value: 5fddab5d-aebe-4b6a-9812-a6edc05c51cc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_138 + identifier: + - value: e65cf53f-41db-4663-97f0-946b98f89312 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008897 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_138_sample_0 + identifier: + - value: f8a73605-d802-4364-aa6e-5d23691f92cf + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008897-6910 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_138_sample_0_subject + identifier: + - value: GENIE-DFCI-008897-6910 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e65cf53f-41db-4663-97f0-946b98f89312 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_139_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_139_diagnosis_0 + identifier: + - value: e769c390-13f6-4054-8182-017360bcfdca + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_139 + identifier: + - value: 1fc0a194-cf52-439f-8bb5-87459fcd4014 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004469 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_139_sample_0 + identifier: + - value: ee78495d-54c1-4d73-93d7-06034b0c7bd0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004469-15 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_139_sample_0_subject + identifier: + - value: GENIE-DFCI-004469-15 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1fc0a194-cf52-439f-8bb5-87459fcd4014 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_140_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_140_diagnosis_0 + identifier: + - value: c8cffdf6-7c37-5146-9bff-2cbd5a6f5bbd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_140 + identifier: + - value: 62887787-9385-470a-a993-98ede58f0940 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7364 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24192 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_140_sample_0 + identifier: + - value: a17406af-2eda-4148-8a0d-ec2ae4bd9fac + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7364-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_140_sample_0_subject + identifier: + - value: TCGA-CR-7364-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 62887787-9385-470a-a993-98ede58f0940 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_140_sample_1 + identifier: + - value: 6ced7677-159f-4e9f-b550-627ab9ea80f7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7364-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_140_sample_1_subject + identifier: + - value: TCGA-CR-7364-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 62887787-9385-470a-a993-98ede58f0940 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_141_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_141_diagnosis_0 + identifier: + - value: 20846d6c-1a34-5e01-a531-f9c783416c3e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_141 + identifier: + - value: aad9a83a-ab62-47b0-990c-527ccdb58d63 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-MZ-A6I9 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24939 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_141_sample_0 + identifier: + - value: 396f116a-bede-472e-847d-435a77dfa7dc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MZ-A6I9-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_141_sample_0_subject + identifier: + - value: TCGA-MZ-A6I9-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aad9a83a-ab62-47b0-990c-527ccdb58d63 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 156 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_141_sample_1 + identifier: + - value: f32ce523-c60e-4a86-bfa0-eeb4f3b2d83a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MZ-A6I9-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_141_sample_1_subject + identifier: + - value: TCGA-MZ-A6I9-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aad9a83a-ab62-47b0-990c-527ccdb58d63 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 156 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_141_sample_2 + identifier: + - value: 0551272d-7e05-435c-92b3-918cde4d14ee + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MZ-A6I9-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_141_sample_2_subject + identifier: + - value: TCGA-MZ-A6I9-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aad9a83a-ab62-47b0-990c-527ccdb58d63 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_142_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_142_diagnosis_0 + identifier: + - value: b588dad7-169a-5ecf-885b-580be11d01cb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_142 + identifier: + - value: 547de7d8-c2f1-41d7-a0b4-cc6f39712301 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6992 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22598 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_142_sample_0 + identifier: + - value: b86352a7-2987-4743-aa3c-1895c438641a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6992-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_142_sample_0_subject + identifier: + - value: TCGA-CN-6992-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 547de7d8-c2f1-41d7-a0b4-cc6f39712301 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_142_sample_1 + identifier: + - value: 7a5921a4-5714-44e7-8ebd-048031b32b88 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6992-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_142_sample_1_subject + identifier: + - value: TCGA-CN-6992-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 547de7d8-c2f1-41d7-a0b4-cc6f39712301 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_142_sample_2 + identifier: + - value: ce0b9c55-baeb-4ca8-9235-51a836a4b58f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6992-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_142_sample_2_subject + identifier: + - value: TCGA-CN-6992-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 547de7d8-c2f1-41d7-a0b4-cc6f39712301 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_143_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_143_diagnosis_0 + identifier: + - value: a08be31b-24b0-5fb3-b49d-955fcce7603c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_143 + identifier: + - value: 3c5bc678-41e9-46b3-9686-5cd95659ab71 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-6827 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20175 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C00.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_143_sample_0 + identifier: + - value: 2ef80e58-961d-45d6-ac3a-a520be3728c9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6827-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_143_sample_0_subject + identifier: + - value: TCGA-D6-6827-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c5bc678-41e9-46b3-9686-5cd95659ab71 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_143_sample_1 + identifier: + - value: 460e7821-2712-4d74-b5a1-b2883b3197ca + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6827-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_143_sample_1_subject + identifier: + - value: TCGA-D6-6827-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c5bc678-41e9-46b3-9686-5cd95659ab71 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_143_sample_2 + identifier: + - value: c53d6135-c614-45f4-8f41-49b20ed4a549 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6827-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_143_sample_2_subject + identifier: + - value: TCGA-D6-6827-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c5bc678-41e9-46b3-9686-5cd95659ab71 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_144_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_144_diagnosis_0 + identifier: + - value: faf259c7-d577-5ef8-9075-9a42f1083260 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_144 + identifier: + - value: 9c128871-1026-46ab-9ae9-7c6aac468b11 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-F7-A622 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27456 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_144_sample_0 + identifier: + - value: 32d7cb3d-5f5a-474a-9dcc-3b5f2dc64d22 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A622-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_144_sample_0_subject + identifier: + - value: TCGA-F7-A622-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9c128871-1026-46ab-9ae9-7c6aac468b11 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_144_sample_1 + identifier: + - value: 3901d8b6-f2f2-45e9-a40f-3ccd679f701e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A622-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_144_sample_1_subject + identifier: + - value: TCGA-F7-A622-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9c128871-1026-46ab-9ae9-7c6aac468b11 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 125 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_144_sample_2 + identifier: + - value: 32056265-c5fb-4544-9f99-22b34febb805 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A622-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_144_sample_2_subject + identifier: + - value: TCGA-F7-A622-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9c128871-1026-46ab-9ae9-7c6aac468b11 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 125 + unit: + coding: *id001 + quantity_collected: + value_decimal: 240 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_145_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_145_diagnosis_0 + identifier: + - value: 5baa4771-eb6d-56d1-821a-33157bf79573 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_145 + identifier: + - value: 16d52afb-a954-4cb3-b168-c1501208f691 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-7866 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14810 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_145_sample_0 + identifier: + - value: fb5ba525-1658-4f8b-81f8-8d7ec3727773 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7866-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_145_sample_0_subject + identifier: + - value: TCGA-BB-7866-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 16d52afb-a954-4cb3-b168-c1501208f691 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_145_sample_1 + identifier: + - value: af5d22cc-87f4-4b91-97bc-7103bc07adcc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7866-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_145_sample_1_subject + identifier: + - value: TCGA-BB-7866-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 16d52afb-a954-4cb3-b168-c1501208f691 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_145_sample_2 + identifier: + - value: 736c3c8c-ff9f-4892-860f-04665a1f344b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7866-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_145_sample_2_subject + identifier: + - value: TCGA-BB-7866-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 16d52afb-a954-4cb3-b168-c1501208f691 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_146_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_146_diagnosis_0 + identifier: + - value: d957f533-9896-5f0b-a9ee-90335d733f67 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_146 + identifier: + - value: f87f7cee-e9bd-45cc-a740-3d8ffa9746d3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-7864 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22317 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_146_sample_0 + identifier: + - value: 1477b393-8acf-4550-86a7-6570c0d7d583 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7864-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_146_sample_0_subject + identifier: + - value: TCGA-BB-7864-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f87f7cee-e9bd-45cc-a740-3d8ffa9746d3 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_146_sample_1 + identifier: + - value: f3c568ae-ad12-4155-a652-8e16e5276bda + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7864-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_146_sample_1_subject + identifier: + - value: TCGA-BB-7864-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f87f7cee-e9bd-45cc-a740-3d8ffa9746d3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_146_sample_2 + identifier: + - value: 4775330f-0409-4bb2-a096-a3d1eb0180d1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7864-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_146_sample_2_subject + identifier: + - value: TCGA-BB-7864-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f87f7cee-e9bd-45cc-a740-3d8ffa9746d3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_147_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_147_diagnosis_0 + identifier: + - value: b56e8d53-a875-5676-8d2d-f095f8b899af + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_147 + identifier: + - value: 4eacd173-025a-442b-8bce-890ccfdca586 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5444 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23650 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2004-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_147_sample_0 + identifier: + - value: 8cc840ea-3053-41a2-a325-6e86f3deeec6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5444-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_147_sample_0_subject + identifier: + - value: TCGA-CV-5444-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4eacd173-025a-442b-8bce-890ccfdca586 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_147_sample_1 + identifier: + - value: 61380e29-a7ae-4e29-b69a-d56f234f1ba0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5444-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_147_sample_1_subject + identifier: + - value: TCGA-CV-5444-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4eacd173-025a-442b-8bce-890ccfdca586 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_147_sample_2 + identifier: + - value: 4deea4a5-4d54-48b2-9a46-68eea668283b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5444-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_147_sample_2_subject + identifier: + - value: TCGA-CV-5444-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4eacd173-025a-442b-8bce-890ccfdca586 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_148_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_148_diagnosis_0 + identifier: + - value: 90bcf4eb-dd05-5d4d-b666-6947b36143d8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_148 + identifier: + - value: b47fb978-2dfb-4abc-a5af-6e14dd684182 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-A6ES + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18408 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_148_sample_0 + identifier: + - value: 59ddae84-32f9-40c0-9d9f-e3b883ab5c47 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6ES-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_148_sample_0_subject + identifier: + - value: TCGA-D6-A6ES-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b47fb978-2dfb-4abc-a5af-6e14dd684182 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_148_sample_1 + identifier: + - value: 0ebb072d-0596-4deb-8607-2548b0396fb0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6ES-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_148_sample_1_subject + identifier: + - value: TCGA-D6-A6ES-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b47fb978-2dfb-4abc-a5af-6e14dd684182 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 69 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_148_sample_2 + identifier: + - value: f99dc3bf-e91d-4011-b62a-2653b53417f0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6ES-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_148_sample_2_subject + identifier: + - value: TCGA-D6-A6ES-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b47fb978-2dfb-4abc-a5af-6e14dd684182 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 69 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_149_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_149_diagnosis_0 + identifier: + - value: bd3c4df6-90f0-58df-8713-51ca36d74124 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_149 + identifier: + - value: 896e37fa-3a6a-481b-b790-5ee62bbdc9fa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A6V3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22397 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_149_sample_0 + identifier: + - value: 97657453-6a97-4879-9440-fd0eea9d5f33 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A6V3-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_149_sample_0_subject + identifier: + - value: TCGA-CN-A6V3-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 896e37fa-3a6a-481b-b790-5ee62bbdc9fa + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 194 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_149_sample_1 + identifier: + - value: 285e2354-8efd-4951-87cf-0e188d11423e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A6V3-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_149_sample_1_subject + identifier: + - value: TCGA-CN-A6V3-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 896e37fa-3a6a-481b-b790-5ee62bbdc9fa + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 194 + unit: + coding: *id001 + quantity_collected: + value_decimal: 230 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_150_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_150_diagnosis_0 + identifier: + - value: 83e6c6d4-83d7-55d8-ab82-aba8f3e543f5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_150 + identifier: + - value: 426a24aa-82c3-42a4-90df-4837871ee286 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6988 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17308 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_150_sample_0 + identifier: + - value: 5bf33753-d3c4-4fbe-a8e0-af958efb6fd1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6988-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_150_sample_0_subject + identifier: + - value: TCGA-CN-6988-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 426a24aa-82c3-42a4-90df-4837871ee286 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_150_sample_1 + identifier: + - value: 4f72ee1e-37e2-4845-90de-812686a25980 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6988-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_150_sample_1_subject + identifier: + - value: TCGA-CN-6988-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 426a24aa-82c3-42a4-90df-4837871ee286 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_150_sample_2 + identifier: + - value: ca2a45b4-1eb0-4e28-a4c8-5647bfbaa98c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6988-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_150_sample_2_subject + identifier: + - value: TCGA-CN-6988-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 426a24aa-82c3-42a4-90df-4837871ee286 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_151_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_151_diagnosis_0 + identifier: + - value: 6ea3680f-baf2-53a3-8308-ae9dfd6ceb1e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_151 + identifier: + - value: 45a10908-19e6-421a-8903-1440bfa57c9d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5355 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23670 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_151_sample_0 + identifier: + - value: 63535469-d402-4ba2-9ab5-986e6ed80f55 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5355-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_151_sample_0_subject + identifier: + - value: TCGA-CN-5355-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 45a10908-19e6-421a-8903-1440bfa57c9d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_151_sample_1 + identifier: + - value: c2ef7833-c2fa-446c-a12e-f353c744b1e4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5355-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_151_sample_1_subject + identifier: + - value: TCGA-CN-5355-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 45a10908-19e6-421a-8903-1440bfa57c9d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_151_sample_2 + identifier: + - value: 256d61e1-54c4-4250-bd17-5bb82496f5f4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5355-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_151_sample_2_subject + identifier: + - value: TCGA-CN-5355-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 45a10908-19e6-421a-8903-1440bfa57c9d + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_152_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_152_diagnosis_0 + identifier: + - value: b27a395e-c9b4-5903-afcf-90ba31fcdeb2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_152 + identifier: + - value: e8ac39e6-377a-412c-b18d-f6c4fc654ec6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-HD-7753 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22774 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_152_sample_0 + identifier: + - value: 7fb56f25-873d-475c-9db6-f0be3945d926 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7753-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_152_sample_0_subject + identifier: + - value: TCGA-HD-7753-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8ac39e6-377a-412c-b18d-f6c4fc654ec6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_152_sample_1 + identifier: + - value: e723f1bb-73a3-4d65-bd25-de76138515e9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7753-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_152_sample_1_subject + identifier: + - value: TCGA-HD-7753-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8ac39e6-377a-412c-b18d-f6c4fc654ec6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_152_sample_2 + identifier: + - value: 698f639f-c34a-4f21-8306-26002008804f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7753-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_152_sample_2_subject + identifier: + - value: TCGA-HD-7753-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8ac39e6-377a-412c-b18d-f6c4fc654ec6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_153_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_153_diagnosis_0 + identifier: + - value: 232f3bad-3cb2-5b4a-91e2-71f37a7eff72 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_153 + identifier: + - value: a71b425b-ccd3-42f0-8163-3721cb1794ef + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A71B + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18404 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_153_sample_0 + identifier: + - value: df66e44f-3130-4d7b-a1d9-2d90f96b4c7e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A71B-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_153_sample_0_subject + identifier: + - value: TCGA-UF-A71B-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a71b425b-ccd3-42f0-8163-3721cb1794ef + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1176 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_153_sample_1 + identifier: + - value: 3a4af2fc-6443-4644-9da0-fee722e6d5c6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A71B-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_153_sample_1_subject + identifier: + - value: TCGA-UF-A71B-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a71b425b-ccd3-42f0-8163-3721cb1794ef + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1071 + unit: + coding: *id001 + quantity_collected: + value_decimal: 80 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_153_sample_2 + identifier: + - value: 5c464f43-4aa0-4203-8828-5fc4cb13cf42 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A71B-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_153_sample_2_subject + identifier: + - value: TCGA-UF-A71B-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a71b425b-ccd3-42f0-8163-3721cb1794ef + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_154_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_154_diagnosis_0 + identifier: + - value: 4b90baa1-cf87-5186-9101-0464aec143d3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_154 + identifier: + - value: 54b295d4-6315-4416-bde7-a221859f965c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A4IG + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 28402 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_154_sample_0 + identifier: + - value: c029272a-feef-4a11-9566-092c16b40eef + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4IG-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_154_sample_0_subject + identifier: + - value: TCGA-BA-A4IG-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 54b295d4-6315-4416-bde7-a221859f965c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 533 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_154_sample_1 + identifier: + - value: ce469c00-b5c0-4d7c-875b-092c5b6ac289 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4IG-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_154_sample_1_subject + identifier: + - value: TCGA-BA-A4IG-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 54b295d4-6315-4416-bde7-a221859f965c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 457 + unit: + coding: *id001 + quantity_collected: + value_decimal: 240 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_155_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_155_diagnosis_0 + identifier: + - value: 3f0b65d8-182e-57af-87b9-29e59fcdaab4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_155 + identifier: + - value: b4d5299d-1f25-4565-b612-0a0a4d6656ec + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-F7-8298 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21445 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_155_sample_0 + identifier: + - value: 3f2ed4ae-5b71-48d9-b120-4f7bfd4b34c4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-8298-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_155_sample_0_subject + identifier: + - value: TCGA-F7-8298-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b4d5299d-1f25-4565-b612-0a0a4d6656ec + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_155_sample_1 + identifier: + - value: 8f5a4b47-4c69-4295-a576-fd3e558754a5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-8298-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_155_sample_1_subject + identifier: + - value: TCGA-F7-8298-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b4d5299d-1f25-4565-b612-0a0a4d6656ec + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_155_sample_2 + identifier: + - value: 94c71079-a453-4a4c-b52a-ab686bc83b65 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-8298-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_155_sample_2_subject + identifier: + - value: TCGA-F7-8298-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b4d5299d-1f25-4565-b612-0a0a4d6656ec + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_156_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_156_diagnosis_0 + identifier: + - value: 37b4b703-52d6-51dd-9cd7-3f759862a78c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_156 + identifier: + - value: 5d5defb3-8572-467d-b383-7358f802b398 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A63W + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17693 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_156_sample_0 + identifier: + - value: 9b9dbf11-d017-4723-a76f-c25ce4a01f09 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63W-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_156_sample_0_subject + identifier: + - value: TCGA-CN-A63W-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d5defb3-8572-467d-b383-7358f802b398 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_156_sample_1 + identifier: + - value: 8da610b4-0a32-4ef8-9f55-1c969addd79f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63W-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_156_sample_1_subject + identifier: + - value: TCGA-CN-A63W-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d5defb3-8572-467d-b383-7358f802b398 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 279 + unit: + coding: *id001 + quantity_collected: + value_decimal: 140 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_156_sample_2 + identifier: + - value: e6cd0e23-4423-4ebb-b314-913419340811 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63W-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_156_sample_2_subject + identifier: + - value: TCGA-CN-A63W-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d5defb3-8572-467d-b383-7358f802b398 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 279 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_157_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_157_diagnosis_0 + identifier: + - value: 6788d692-193d-5d61-975f-1a79e54439ff + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_157 + identifier: + - value: e4733700-ff23-43ff-bfa0-e679ce9352c9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-6516 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25242 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C00.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_157_sample_0 + identifier: + - value: 2d8d11be-421d-4f96-b5d6-4cbc632f11f3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6516-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_157_sample_0_subject + identifier: + - value: TCGA-D6-6516-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e4733700-ff23-43ff-bfa0-e679ce9352c9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_157_sample_1 + identifier: + - value: c129394b-3c04-4a6a-b4ea-d56d96bf28ef + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6516-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_157_sample_1_subject + identifier: + - value: TCGA-D6-6516-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e4733700-ff23-43ff-bfa0-e679ce9352c9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_157_sample_2 + identifier: + - value: c3c82c51-0200-44c8-b5aa-050084983398 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6516-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_157_sample_2_subject + identifier: + - value: TCGA-D6-6516-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e4733700-ff23-43ff-bfa0-e679ce9352c9 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_158_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_158_diagnosis_0 + identifier: + - value: c061cf11-1e3a-5906-b58b-2b5530a456fd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_158 + identifier: + - value: 730c3b27-24d5-4a80-b659-db54cd2bc4fa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-6870 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22222 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_158_sample_0 + identifier: + - value: cc1be5d1-ea6a-4e7d-822b-51887dab88b6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6870-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_158_sample_0_subject + identifier: + - value: TCGA-BA-6870-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 730c3b27-24d5-4a80-b659-db54cd2bc4fa + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_158_sample_1 + identifier: + - value: e6af426a-d899-44ef-96a8-92bd76a0ea3a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6870-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_158_sample_1_subject + identifier: + - value: TCGA-BA-6870-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 730c3b27-24d5-4a80-b659-db54cd2bc4fa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_158_sample_2 + identifier: + - value: 5bf05a41-3a19-445b-96bd-439b9cac01eb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6870-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_158_sample_2_subject + identifier: + - value: TCGA-BA-6870-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 730c3b27-24d5-4a80-b659-db54cd2bc4fa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_159_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_159_diagnosis_0 + identifier: + - value: 7c9e489a-67bb-5aef-92cb-b776ab07f413 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_159 + identifier: + - value: 1acda00d-04fb-4d71-99a4-996f92601827 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-A6EQ + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20876 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_159_sample_0 + identifier: + - value: 37e8e5f5-0edb-420a-9f32-a2e167ef4cf4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EQ-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_159_sample_0_subject + identifier: + - value: TCGA-D6-A6EQ-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1acda00d-04fb-4d71-99a4-996f92601827 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_159_sample_1 + identifier: + - value: 041d7de0-fdee-4f6b-9945-058f8bab509c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EQ-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_159_sample_1_subject + identifier: + - value: TCGA-D6-A6EQ-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1acda00d-04fb-4d71-99a4-996f92601827 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 86 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_159_sample_2 + identifier: + - value: 43a91c60-f1f5-4b10-b0ee-c55afadac481 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EQ-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_159_sample_2_subject + identifier: + - value: TCGA-D6-A6EQ-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1acda00d-04fb-4d71-99a4-996f92601827 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 86 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_160_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_160_diagnosis_0 + identifier: + - value: afec3d92-5a3c-5b04-a2f1-49031942cc1d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_160 + identifier: + - value: c1f286f6-d4a1-494a-88c8-ff8e2a3df2ce + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A6IH + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23936 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_160_sample_0 + identifier: + - value: 63b4690f-f247-4874-9923-e96375c56a01 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6IH-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_160_sample_0_subject + identifier: + - value: TCGA-QK-A6IH-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c1f286f6-d4a1-494a-88c8-ff8e2a3df2ce + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 38 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_160_sample_1 + identifier: + - value: 5f210369-1839-4f18-b081-974efc7de032 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6IH-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_160_sample_1_subject + identifier: + - value: TCGA-QK-A6IH-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c1f286f6-d4a1-494a-88c8-ff8e2a3df2ce + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_160_sample_2 + identifier: + - value: 0d0194eb-d83f-4028-9b4b-3308c0207133 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6IH-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_160_sample_2_subject + identifier: + - value: TCGA-QK-A6IH-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c1f286f6-d4a1-494a-88c8-ff8e2a3df2ce + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 38 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_161_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_161_diagnosis_0 + identifier: + - value: 35b1cfb8-bac8-5abb-85dc-1761cd25e90c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_161 + identifier: + - value: 451e4916-80ee-45f8-ad70-84340868a5a9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A5Q6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17917 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2005-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_161_sample_0 + identifier: + - value: 1ac65133-fc2b-4b41-a101-eacd225f71b1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5Q6-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_161_sample_0_subject + identifier: + - value: TCGA-P3-A5Q6-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 451e4916-80ee-45f8-ad70-84340868a5a9 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_161_sample_1 + identifier: + - value: b929bf9b-34a0-4fa3-9bd5-49f8097c573e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5Q6-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_161_sample_1_subject + identifier: + - value: TCGA-P3-A5Q6-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 451e4916-80ee-45f8-ad70-84340868a5a9 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 2922 + unit: + coding: *id001 + quantity_collected: + value_decimal: 10 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_161_sample_2 + identifier: + - value: 73005780-ea15-4353-b6f7-c26865d3f4d0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5Q6-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_161_sample_2_subject + identifier: + - value: TCGA-P3-A5Q6-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 451e4916-80ee-45f8-ad70-84340868a5a9 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 2922 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_162_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_162_diagnosis_0 + identifier: + - value: e7f08842-7c61-469c-829a-feff82339bee + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_162 + identifier: + - value: 70a1ed54-35ce-4466-b4c3-72e2f68ed3bd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008328 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_162_sample_0 + identifier: + - value: 6d1a6236-3625-4300-9f12-4e666cb2694a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008328-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_162_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008328-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 70a1ed54-35ce-4466-b4c3-72e2f68ed3bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_163_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_163_diagnosis_0 + identifier: + - value: 6252ba82-08cf-4a88-892e-bd2847842225 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_163 + identifier: + - value: 6d5068a1-2fd4-4d50-a0bf-f4a6f6badaeb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0009588 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_163_sample_0 + identifier: + - value: 0fd4a1fd-2313-475e-ae01-d424516e42c9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0009588-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_163_sample_0_subject + identifier: + - value: GENIE-MSK-P-0009588-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6d5068a1-2fd4-4d50-a0bf-f4a6f6badaeb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_164_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_164_diagnosis_0 + identifier: + - value: 509526cc-f60a-4e6d-8a18-2f76ba8e995c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_164 + identifier: + - value: 86fc8af5-b98d-440c-b992-46c75cffe6c6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000586 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_164_sample_0 + identifier: + - value: 6d54051a-c75c-40e6-9215-3e470f0d242e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000586-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_164_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000586-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 86fc8af5-b98d-440c-b992-46c75cffe6c6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_165_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_165_diagnosis_0 + identifier: + - value: 5ba2b63c-b0c8-4304-820c-9b04ebb5a7fc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_165 + identifier: + - value: 9d4f373b-99db-4a5d-a37a-0faeb43d2ef0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-002837 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_165_sample_0 + identifier: + - value: fb20acec-aeb5-4591-b114-0834c6629db7 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-002837-2078 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_165_sample_0_subject + identifier: + - value: GENIE-DFCI-002837-2078 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9d4f373b-99db-4a5d-a37a-0faeb43d2ef0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_166_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_166_diagnosis_0 + identifier: + - value: 58498007-02e8-41fb-b884-2383b5eb1414 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_166 + identifier: + - value: cc6e8ea7-4884-46c8-bb89-f04ef33fba0d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007582 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_166_sample_0 + identifier: + - value: f198873e-fb8b-4ddb-8d79-1fcf1bb1d764 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007582-3990 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_166_sample_0_subject + identifier: + - value: GENIE-DFCI-007582-3990 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cc6e8ea7-4884-46c8-bb89-f04ef33fba0d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_167_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_167_diagnosis_0 + identifier: + - value: e980228b-ecef-406e-91da-09bc06d5ad04 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_167 + identifier: + - value: 85dfbb2c-83b1-493a-b643-f9d4afe0f7c4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-000968 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_167_sample_0 + identifier: + - value: 37ecc052-0274-45dd-98db-fb0d5476fa16 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-000968-1363 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_167_sample_0_subject + identifier: + - value: GENIE-DFCI-000968-1363 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 85dfbb2c-83b1-493a-b643-f9d4afe0f7c4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_168_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_168_diagnosis_0 + identifier: + - value: 2a826dce-5a83-46e6-8ff0-9c7597ff54d4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_168 + identifier: + - value: 39ac5cb7-05a4-49eb-811d-7c9a5e4f8579 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-673077 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_168_sample_0 + identifier: + - value: a5fa104a-bb1e-4e7d-a740-607fc803f4f3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-673077-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_168_sample_0_subject + identifier: + - value: GENIE-VICC-673077-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 39ac5cb7-05a4-49eb-811d-7c9a5e4f8579 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_169_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_169_diagnosis_0 + identifier: + - value: 0099f9fb-0d9a-46a0-a86f-c10dd58ad440 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_169 + identifier: + - value: 3067a0b7-4cf2-4cc8-92e2-ebbefd0b667a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD8066 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 8266 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_169_sample_0 + identifier: + - value: dc97ccf6-b026-45ac-a658-fb44806230a1 + system: http://crdc.nci.nih.gov/gdc + - value: AD8066_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_169_sample_0_subject + identifier: + - value: AD8066_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3067a0b7-4cf2-4cc8-92e2-ebbefd0b667a + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_170_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_170_diagnosis_0 + identifier: + - value: c508644c-d496-4647-a065-4e0077d99b67 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_170 + identifier: + - value: 0f16979d-c19c-4e16-9b51-ecab830717cd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008357 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_170_sample_0 + identifier: + - value: 80c31730-c365-4f43-ae30-d082f4c7f67a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008357-5599 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_170_sample_0_subject + identifier: + - value: GENIE-DFCI-008357-5599 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0f16979d-c19c-4e16-9b51-ecab830717cd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_171_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_171_diagnosis_0 + identifier: + - value: 155420b6-0bc4-42f0-a28d-863e56f9e200 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_171 + identifier: + - value: 750966b1-b299-48be-ae85-a7984d33b91b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD864 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 7505 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_171_sample_0 + identifier: + - value: 24318871-5bfe-4bbe-8df8-9e415558ae47 + system: http://crdc.nci.nih.gov/gdc + - value: AD864_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_171_sample_0_subject + identifier: + - value: AD864_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 750966b1-b299-48be-ae85-a7984d33b91b + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_172_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_172_diagnosis_0 + identifier: + - value: efe7297e-9961-4ac3-b247-a9322e18240c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_172 + identifier: + - value: 514f981b-b3e4-454e-b9b6-8ec17c4f9931 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD16071 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19541 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_172_sample_0 + identifier: + - value: 542b7dd6-20ad-4719-bece-768060ddab97 + system: http://crdc.nci.nih.gov/gdc + - value: AD16071_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_172_sample_0_subject + identifier: + - value: AD16071_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 514f981b-b3e4-454e-b9b6-8ec17c4f9931 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_173_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_173_diagnosis_0 + identifier: + - value: 203f4d20-b796-4745-9bc0-6385c28ff0ba + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_173 + identifier: + - value: 62d14c0a-e785-44c6-a7a8-9ccd5b881259 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003320 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_173_sample_0 + identifier: + - value: 3a006479-c2eb-457a-b0a1-e3faebae25b9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003320-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_173_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003320-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 62d14c0a-e785-44c6-a7a8-9ccd5b881259 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_174_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_174_diagnosis_0 + identifier: + - value: 696fd614-355c-42d4-b318-9d4a0d23ee17 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_174 + identifier: + - value: 9c82af9b-df83-498e-9cd5-4ed246d58ab0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-001641 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_174_sample_0 + identifier: + - value: 14dd72d1-596c-42c6-a5aa-c3220dc6fc21 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-001641-3996 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_174_sample_0_subject + identifier: + - value: GENIE-DFCI-001641-3996 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9c82af9b-df83-498e-9cd5-4ed246d58ab0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_175_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_175_diagnosis_0 + identifier: + - value: d4b595ef-5e2f-4722-bf4e-48bb831bc057 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_175 + identifier: + - value: 3050b713-c173-40ff-a4e7-30e7a5ded8c0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-002065 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_175_sample_0 + identifier: + - value: 172019a6-18cf-4532-89ec-9f4ec83dee30 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-002065-124 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_175_sample_0_subject + identifier: + - value: GENIE-DFCI-002065-124 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3050b713-c173-40ff-a4e7-30e7a5ded8c0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_176_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_176_diagnosis_0 + identifier: + - value: 56566536-d3a4-4103-bd5b-550ceaad2a6b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_176 + identifier: + - value: c2415d77-732b-43b7-9a70-53e2bc708686 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5017 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20089 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_176_sample_0 + identifier: + - value: e2edc535-6fc4-4999-aa4c-932bf58d344e + system: http://crdc.nci.nih.gov/gdc + - value: AD5017_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_176_sample_0_subject + identifier: + - value: AD5017_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c2415d77-732b-43b7-9a70-53e2bc708686 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_177_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_177_diagnosis_0 + identifier: + - value: 671671bc-dbf4-4e15-b978-6aceaac1533f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_177 + identifier: + - value: 55f39187-e51c-4f7b-bd3e-ea26c7e3ba4b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0016761 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_177_sample_0 + identifier: + - value: 0d989563-7a49-49e9-9417-4b607d661ab4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0016761-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_177_sample_0_subject + identifier: + - value: GENIE-MSK-P-0016761-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 55f39187-e51c-4f7b-bd3e-ea26c7e3ba4b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_178_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_178_diagnosis_0 + identifier: + - value: 523155c1-e181-4d6f-9873-9449a8e3c289 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_178 + identifier: + - value: a1ada018-67e0-4c0e-9efe-f2d3e7476b91 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-036955 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_178_sample_0 + identifier: + - value: 9ed6f000-4643-4f65-be84-8fd380d3bc36 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-036955-74886 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_178_sample_0_subject + identifier: + - value: GENIE-DFCI-036955-74886 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a1ada018-67e0-4c0e-9efe-f2d3e7476b91 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_179_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_179_diagnosis_0 + identifier: + - value: a0943f40-a682-4318-bc07-eea80150867b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_179 + identifier: + - value: 281b006b-7671-4253-8c53-a4e310ecfe15 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037288 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_179_sample_0 + identifier: + - value: 8449ccd3-033e-4c9f-bec5-9f341264e12b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037288-116439 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_179_sample_0_subject + identifier: + - value: GENIE-DFCI-037288-116439 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 281b006b-7671-4253-8c53-a4e310ecfe15 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_180_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_180_diagnosis_0 + identifier: + - value: 11f5b868-a6eb-4575-b5d4-54cd8a406293 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_180 + identifier: + - value: cf783624-ff25-4474-861f-4695935678f1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-027923 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_180_sample_0 + identifier: + - value: 4e763f63-0494-4b2f-9f6a-c9461c7e7b1e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-027923-87624 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_180_sample_0_subject + identifier: + - value: GENIE-DFCI-027923-87624 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cf783624-ff25-4474-861f-4695935678f1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_181_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_181_diagnosis_0 + identifier: + - value: d7acd35e-0ca1-42f0-932c-a3cdd6f8d09b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_181 + identifier: + - value: c8085cd6-cf74-4b86-96a7-bdc43f2e8c83 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037833 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_181_sample_0 + identifier: + - value: 8f775235-6026-40f6-b156-cc3711222412 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037833-36073 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_181_sample_0_subject + identifier: + - value: GENIE-DFCI-037833-36073 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c8085cd6-cf74-4b86-96a7-bdc43f2e8c83 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_182_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_182_diagnosis_0 + identifier: + - value: 78608de5-dd5b-43da-8934-e0b6fa924ab4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_182 + identifier: + - value: 1fb48d35-0b87-4614-a309-aa71bada9a0f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-4493 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_182_sample_0 + identifier: + - value: 8955be34-dfc4-4a5e-9636-f27ccef4318a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-4493-11651 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_182_sample_0_subject + identifier: + - value: GENIE-MDA-4493-11651 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1fb48d35-0b87-4614-a309-aa71bada9a0f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_183_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_183_diagnosis_0 + identifier: + - value: d8e6b6ed-5c11-4a78-b25a-07f23305bb40 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_183 + identifier: + - value: 11165da5-e165-486a-8c37-c9bdd779344d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-6285 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_183_sample_0 + identifier: + - value: 8479ff0a-fce8-4f4e-8d00-6775d1e9cb00 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-6285-17334 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_183_sample_0_subject + identifier: + - value: GENIE-MDA-6285-17334 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 11165da5-e165-486a-8c37-c9bdd779344d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_184_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_184_diagnosis_0 + identifier: + - value: 64bd8ea3-d4cf-4e2c-9d2e-77dcadd5364b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_184 + identifier: + - value: 614b017b-a51c-4ba6-9d0c-9b5b22b73901 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008227 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_184_sample_0 + identifier: + - value: 2386e3a8-c4ea-4434-af11-e60fae9630fc + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008227-5962 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_184_sample_0_subject + identifier: + - value: GENIE-DFCI-008227-5962 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 614b017b-a51c-4ba6-9d0c-9b5b22b73901 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_185_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_185_diagnosis_0 + identifier: + - value: f87fc232-ea15-4a26-a863-8604cdb8bb06 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_185 + identifier: + - value: 60fc8a2b-eb0a-44e9-81ed-e443045d4557 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037287 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_185_sample_0 + identifier: + - value: 421f819b-c4ac-445f-882d-c36766f7002a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037287-88492 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_185_sample_0_subject + identifier: + - value: GENIE-DFCI-037287-88492 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 60fc8a2b-eb0a-44e9-81ed-e443045d4557 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_186_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_186_diagnosis_0 + identifier: + - value: a69046f9-49c2-4846-a394-ffebf61b0340 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_186 + identifier: + - value: 89eeb00c-fed5-42f1-9aeb-03d0acca36e8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-001847 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_186_sample_0 + identifier: + - value: ae00c91b-f03b-41fa-bd2f-d6fde4338cf1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-001847-1155 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_186_sample_0_subject + identifier: + - value: GENIE-DFCI-001847-1155 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 89eeb00c-fed5-42f1-9aeb-03d0acca36e8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_187_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_187_diagnosis_0 + identifier: + - value: 38c088b1-bab2-4d5c-8f45-80280d1c309b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_187 + identifier: + - value: 864ee6c8-dc5a-4eb1-acc9-52390116dbfb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010800 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_187_sample_0 + identifier: + - value: b480938b-4562-4d37-a280-16cd4dc700ca + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010800-9387 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_187_sample_0_subject + identifier: + - value: GENIE-DFCI-010800-9387 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 864ee6c8-dc5a-4eb1-acc9-52390116dbfb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_188_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_188_diagnosis_0 + identifier: + - value: fc929f30-0322-43c4-b12f-ddff9d8a2335 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_188 + identifier: + - value: 5c3017f9-63e1-4f81-9d1d-4d5f4814b07c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010590 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_188_sample_0 + identifier: + - value: 175e9244-58cb-4b1a-9614-a4fb1c0e6603 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010590-8636 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_188_sample_0_subject + identifier: + - value: GENIE-DFCI-010590-8636 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5c3017f9-63e1-4f81-9d1d-4d5f4814b07c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_189_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_189_diagnosis_0 + identifier: + - value: 47d4038e-908a-40b8-8a91-7bdcc4421624 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_189 + identifier: + - value: 9e190f34-a92a-4019-a9bf-757ddfb7aa4e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007857 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_189_sample_0 + identifier: + - value: 01a0cb84-c716-4134-aa16-ef008ae30469 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007857-7172 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_189_sample_0_subject + identifier: + - value: GENIE-DFCI-007857-7172 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9e190f34-a92a-4019-a9bf-757ddfb7aa4e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_190_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_190_diagnosis_0 + identifier: + - value: c740d9c9-bb4f-4ae0-9920-43267c9bc180 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_190 + identifier: + - value: 92104e11-d832-461f-bd72-022a67c627dc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD14561 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20148 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_190_sample_0 + identifier: + - value: 97cac184-023d-4aaf-9637-cc34969471cb + system: http://crdc.nci.nih.gov/gdc + - value: AD14561_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_190_sample_0_subject + identifier: + - value: AD14561_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 92104e11-d832-461f-bd72-022a67c627dc + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_191_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_191_diagnosis_0 + identifier: + - value: 59474381-516a-4be2-8b74-7fe5804ec371 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_191 + identifier: + - value: de394ead-1e41-4840-87cf-4c72cc2cb6cb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003795 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_191_sample_0 + identifier: + - value: 8212fb32-9c81-4bf1-ab6b-337196acdf90 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003795-3691 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_191_sample_0_subject + identifier: + - value: GENIE-DFCI-003795-3691 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: de394ead-1e41-4840-87cf-4c72cc2cb6cb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_192_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_192_diagnosis_0 + identifier: + - value: ad265c45-3ba4-4f8a-afcd-70d7f2e79751 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_192 + identifier: + - value: aed0795b-e58b-449c-8202-162cebbaaedc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009344 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_192_sample_0 + identifier: + - value: b993e287-e823-4843-b182-3bf775dfb489 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009344-6546 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_192_sample_0_subject + identifier: + - value: GENIE-DFCI-009344-6546 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aed0795b-e58b-449c-8202-162cebbaaedc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_193_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_193_diagnosis_0 + identifier: + - value: fbf35ed3-c5af-4591-88be-e9971b7d40f6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_193 + identifier: + - value: c1677a28-0d45-4abd-b6a3-9dc6e4cf4be6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-053418 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_193_sample_0 + identifier: + - value: a3b9c3f7-8499-4c17-92f9-274b1ee52764 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-053418-203556 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_193_sample_0_subject + identifier: + - value: GENIE-DFCI-053418-203556 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c1677a28-0d45-4abd-b6a3-9dc6e4cf4be6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_194_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_194_diagnosis_0 + identifier: + - value: 6d395db6-3f58-4c4a-82dd-9b3b9c35fc8f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_194 + identifier: + - value: 6809e2ac-8a49-4352-999f-f7511f4f35e2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004670 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_194_sample_0 + identifier: + - value: 3396e2a0-10bb-43b3-b5be-7980064889e0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004670-873 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_194_sample_0_subject + identifier: + - value: GENIE-DFCI-004670-873 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6809e2ac-8a49-4352-999f-f7511f4f35e2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_195_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_195_diagnosis_0 + identifier: + - value: 6176f8de-0835-4f23-9ce1-85511ac4e1f9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_195 + identifier: + - value: adc64624-5175-4823-b1e5-857f92685dcc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD7774 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17216 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_195_sample_0 + identifier: + - value: bcecf093-e764-4c32-81e5-619d0e86216e + system: http://crdc.nci.nih.gov/gdc + - value: AD7774_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_195_sample_0_subject + identifier: + - value: AD7774_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: adc64624-5175-4823-b1e5-857f92685dcc + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_196_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_196_diagnosis_0 + identifier: + - value: fac35228-e5eb-403f-a9fd-c88a2518c7c1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_196 + identifier: + - value: 2add968d-b2a1-483f-a5e6-e7a71af3acfe + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009544 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_196_sample_0 + identifier: + - value: 933ddbda-c8bb-4e81-9342-9d7379bd6332 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009544-8452 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_196_sample_0_subject + identifier: + - value: GENIE-DFCI-009544-8452 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2add968d-b2a1-483f-a5e6-e7a71af3acfe + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_197_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_197_diagnosis_0 + identifier: + - value: 0e8b9b8f-041a-4d83-8af0-503b7d84e00a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_197 + identifier: + - value: 88996050-399c-472c-a759-91a1a8378213 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD4383 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 16792 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_197_sample_0 + identifier: + - value: ea5776ba-c4cc-4d4b-9e33-573ea824853a + system: http://crdc.nci.nih.gov/gdc + - value: AD4383_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_197_sample_0_subject + identifier: + - value: AD4383_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 88996050-399c-472c-a759-91a1a8378213 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_198_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_198_diagnosis_0 + identifier: + - value: b03c5a4b-9dd8-4186-b8d5-a65acb317474 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_198 + identifier: + - value: 8b7e13be-88dc-4622-b499-f7fa46faa298 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD3459 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26493 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_198_sample_0 + identifier: + - value: c54fca3a-3919-4ac7-81b6-f1cf955f47a7 + system: http://crdc.nci.nih.gov/gdc + - value: AD3459_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_198_sample_0_subject + identifier: + - value: AD3459_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8b7e13be-88dc-4622-b499-f7fa46faa298 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_199_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_199_diagnosis_0 + identifier: + - value: 583cb32e-5e1c-4f3a-bdef-035629e3eb57 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_199 + identifier: + - value: 05ff6947-a8fb-4cd9-b915-5c6d7bb27b71 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5451 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27365 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_199_sample_0 + identifier: + - value: a8ae1d5d-04b7-4012-9bf5-70a664f325ee + system: http://crdc.nci.nih.gov/gdc + - value: AD5451_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_199_sample_0_subject + identifier: + - value: AD5451_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 05ff6947-a8fb-4cd9-b915-5c6d7bb27b71 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_200_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_200_diagnosis_0 + identifier: + - value: b4c405c4-ece9-4cd9-b11c-cb1f863021cb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_200 + identifier: + - value: 65809acd-bab5-4bf9-ab54-f739a29ef960 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003788 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_200_sample_0 + identifier: + - value: f933f399-d986-43eb-bdc0-b3faf49bf513 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003788-772 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_200_sample_0_subject + identifier: + - value: GENIE-DFCI-003788-772 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 65809acd-bab5-4bf9-ab54-f739a29ef960 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_201_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_201_diagnosis_0 + identifier: + - value: bbbf3549-d0cf-4dcc-bc92-32d12cd2c96b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_201 + identifier: + - value: bbaed019-c813-4e3b-af34-03d44d9a92a6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD10083 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22699 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_201_sample_0 + identifier: + - value: 712ad6f8-8c2a-4c82-a89a-10ff849e3e9e + system: http://crdc.nci.nih.gov/gdc + - value: AD10083_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_201_sample_0_subject + identifier: + - value: AD10083_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: bbaed019-c813-4e3b-af34-03d44d9a92a6 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_202_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_202_diagnosis_0 + identifier: + - value: cae73de1-65ae-48fb-a08c-355e6921dca5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_202 + identifier: + - value: 8b124c83-ef2e-44d5-9513-235b36b3bf10 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006462 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_202_sample_0 + identifier: + - value: f632701a-5242-4839-b96d-0214c7e9a73e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006462-4354 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_202_sample_0_subject + identifier: + - value: GENIE-DFCI-006462-4354 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8b124c83-ef2e-44d5-9513-235b36b3bf10 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_203_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_203_diagnosis_0 + identifier: + - value: ad342355-cfa9-458f-8723-7a099368b797 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_203 + identifier: + - value: a77c4788-0c81-4d34-959a-8b82853e6ef8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008794 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_203_sample_0 + identifier: + - value: 536ca98b-7415-49d8-84c2-dca4b5070ff6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008794-7198 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_203_sample_0_subject + identifier: + - value: GENIE-DFCI-008794-7198 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a77c4788-0c81-4d34-959a-8b82853e6ef8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_204_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_204_diagnosis_0 + identifier: + - value: 5db2900f-3088-48fa-ad1c-8dbba6bedbef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_204 + identifier: + - value: ba0cdde3-77ce-48b1-a2fe-ae69759ba759 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0017777 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_204_sample_0 + identifier: + - value: dc326cf0-cb20-4f0a-968a-28c6923319dd + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0017777-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_204_sample_0_subject + identifier: + - value: GENIE-MSK-P-0017777-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ba0cdde3-77ce-48b1-a2fe-ae69759ba759 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_205_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_205_diagnosis_0 + identifier: + - value: 10fdde54-4aab-4498-925c-38ccd8df431d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_205 + identifier: + - value: 7da4cfb5-19db-4c2a-9a2b-0850cb006df6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015591 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_205_sample_0 + identifier: + - value: d2928928-ad9f-46d3-89a5-a00131eaec79 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015591-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_205_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015591-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7da4cfb5-19db-4c2a-9a2b-0850cb006df6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_206_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_206_diagnosis_0 + identifier: + - value: 75ebf700-6ff1-4980-a420-41df37dd2c42 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_206 + identifier: + - value: 1a3f13f4-ef32-4e15-93fe-49008040643a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0018608 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_206_sample_0 + identifier: + - value: e4d9ec72-9281-4b2e-841d-06d84634968d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0018608-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_206_sample_0_subject + identifier: + - value: GENIE-MSK-P-0018608-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1a3f13f4-ef32-4e15-93fe-49008040643a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_207_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_207_diagnosis_0 + identifier: + - value: f8933756-4001-4c7b-94c7-2d8964ffda9e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_207 + identifier: + - value: 377d207c-3315-4e4e-b9ef-f991ba37fa61 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005118 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_207_sample_0 + identifier: + - value: 430338db-7df9-43c8-be80-6ef5a6b98899 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005118-1198 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_207_sample_0_subject + identifier: + - value: GENIE-DFCI-005118-1198 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 377d207c-3315-4e4e-b9ef-f991ba37fa61 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_208_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_208_diagnosis_0 + identifier: + - value: c8d65c8c-9299-49bc-bfe0-97c19ff35fd2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_208 + identifier: + - value: f64aa491-4d35-4341-a39b-8a0ddf38c980 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037050 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_208_sample_0 + identifier: + - value: 58a5858d-4740-4da1-8959-43d7b05ae1ea + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037050-88705 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_208_sample_0_subject + identifier: + - value: GENIE-DFCI-037050-88705 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f64aa491-4d35-4341-a39b-8a0ddf38c980 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_209_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_209_diagnosis_0 + identifier: + - value: 83347eee-7d6a-4848-a139-a71f053e92c9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_209 + identifier: + - value: 90e53226-a6fb-46de-badc-8cb7054b7f06 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000768 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_209_sample_0 + identifier: + - value: fd2acd96-a021-4fd4-b0f5-1d9f6e4448bb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000768-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_209_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000768-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 90e53226-a6fb-46de-badc-8cb7054b7f06 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_210_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_210_diagnosis_0 + identifier: + - value: 2fcaff59-bc46-4971-9a75-dcbf2c85a5ca + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_210 + identifier: + - value: 9b9a3195-ac74-4619-a2c4-35aa5f22f33d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0013498 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_210_sample_0 + identifier: + - value: 1c156e43-c8c3-4ecb-83ff-2075ebd89cd7 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0013498-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_210_sample_0_subject + identifier: + - value: GENIE-MSK-P-0013498-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9b9a3195-ac74-4619-a2c4-35aa5f22f33d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_211_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_211_diagnosis_0 + identifier: + - value: 6d9a9668-da18-4c45-a108-8b0b058ec47c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_211 + identifier: + - value: e271e55b-2033-47ab-bd85-4e880f993671 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006284 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_211_sample_0 + identifier: + - value: 6b2d8256-f78a-4ac8-b0c3-a97a03410b59 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006284-4777 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_211_sample_0_subject + identifier: + - value: GENIE-DFCI-006284-4777 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e271e55b-2033-47ab-bd85-4e880f993671 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_212_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_212_diagnosis_0 + identifier: + - value: 5b518f0a-dbef-4346-b463-b59bd735a311 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_212 + identifier: + - value: e66057bd-8bd4-47d9-8b4d-beab011490c4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009367 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_212_sample_0 + identifier: + - value: 7230cf9f-1930-4377-bfdb-6e07cd472bc0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009367-8081 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_212_sample_0_subject + identifier: + - value: GENIE-DFCI-009367-8081 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e66057bd-8bd4-47d9-8b4d-beab011490c4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_213_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_213_diagnosis_0 + identifier: + - value: 982f892f-104c-4948-8788-6c77775e53a7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_213 + identifier: + - value: f6890daf-37d3-4f5a-af33-ca458c30b0ed + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-013165 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_213_sample_0 + identifier: + - value: 27e33c39-2025-4573-9b0c-1bc774566bfa + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-013165-23146 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_213_sample_0_subject + identifier: + - value: GENIE-DFCI-013165-23146 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f6890daf-37d3-4f5a-af33-ca458c30b0ed + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_214_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_214_diagnosis_0 + identifier: + - value: 6f1ab30c-67b7-4a7f-b4ef-22b1221bec7d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_214 + identifier: + - value: e6a385ac-df27-4e19-ade7-0215f7d47590 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0012422 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_214_sample_0 + identifier: + - value: e125a436-ca27-4a85-bd9d-9ca108306229 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0012422-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_214_sample_0_subject + identifier: + - value: GENIE-MSK-P-0012422-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e6a385ac-df27-4e19-ade7-0215f7d47590 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_215_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_215_diagnosis_0 + identifier: + - value: 43212ae1-0d0a-411e-8ae0-61de91147afe + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_215 + identifier: + - value: 000bddf2-20df-4322-8bd0-67e1959b786d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006740 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_215_sample_0 + identifier: + - value: 5f316e98-9980-4841-b297-f07b3e87004f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006740-7890 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_215_sample_0_subject + identifier: + - value: GENIE-DFCI-006740-7890 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 000bddf2-20df-4322-8bd0-67e1959b786d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_216_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_216_diagnosis_0 + identifier: + - value: 230d872b-0206-409c-988e-6485dae90db9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_216 + identifier: + - value: 1919e513-f8e4-4463-9ed4-5268eff25afa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-p8qm5k95 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_216_sample_0 + identifier: + - value: 2d54eff7-a093-4bf0-b1c2-2f9f159e6b78 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-p8qm5k95-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_216_sample_0_subject + identifier: + - value: GENIE-GRCC-p8qm5k95-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1919e513-f8e4-4463-9ed4-5268eff25afa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_217_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_217_diagnosis_0 + identifier: + - value: c34f7850-ab91-4173-b716-b487c290ec78 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_217 + identifier: + - value: c21fc9a1-f064-4059-98a3-562dacbeafd9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0012862 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_217_sample_0 + identifier: + - value: 59d43c02-f731-4a7f-97ae-c3d7dac2d5e0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0012862-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_217_sample_0_subject + identifier: + - value: GENIE-MSK-P-0012862-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c21fc9a1-f064-4059-98a3-562dacbeafd9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_218_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_218_diagnosis_0 + identifier: + - value: 5cb1278d-4b33-401c-b200-b4408788c927 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_218 + identifier: + - value: cc0fb556-148e-4812-859f-ce0ea8ac2d8b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-002669 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_218_sample_0 + identifier: + - value: 4d69eeb9-81bd-4146-9a4a-3ca86c789272 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-002669-7683 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_218_sample_0_subject + identifier: + - value: GENIE-DFCI-002669-7683 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cc0fb556-148e-4812-859f-ce0ea8ac2d8b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_219_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_219_diagnosis_0 + identifier: + - value: cb8fb063-f8b5-4748-b937-5efb6fefecfc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_219 + identifier: + - value: 8ca01026-6ccf-4be9-b675-ee887ccbdbc7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004149 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_219_sample_0 + identifier: + - value: e331b564-d79c-446d-bff2-a732dacba6bb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004149-1026 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_219_sample_0_subject + identifier: + - value: GENIE-DFCI-004149-1026 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8ca01026-6ccf-4be9-b675-ee887ccbdbc7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_220_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_220_diagnosis_0 + identifier: + - value: f773f13c-c661-46fd-8bd1-56dae4502465 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_220 + identifier: + - value: f40ec72b-e8f0-4a47-80ae-beda3e2fe4ed + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-8057 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_220_sample_0 + identifier: + - value: 2af6ce71-3d6c-4da8-8b75-f0ae49f95bd2 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-8057-18231 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_220_sample_0_subject + identifier: + - value: GENIE-MDA-8057-18231 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f40ec72b-e8f0-4a47-80ae-beda3e2fe4ed + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_221_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_221_diagnosis_0 + identifier: + - value: 5a157d1d-a316-4b42-8444-63e22ee704ec + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_221 + identifier: + - value: 1d565b76-540e-4ecf-8353-6f3fb6c0b762 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-065d55ae + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_221_sample_0 + identifier: + - value: 7128ab9a-3a2d-4df6-8604-829406ab3bed + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-065d55ae-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_221_sample_0_subject + identifier: + - value: GENIE-GRCC-065d55ae-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1d565b76-540e-4ecf-8353-6f3fb6c0b762 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_222_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_222_diagnosis_0 + identifier: + - value: fc0ee2ab-b738-49c2-b645-4b6851be5e8b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_222 + identifier: + - value: 1f92d968-687e-42bc-a4fc-da0f6c8f6eb9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-49d6a6ea + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_222_sample_0 + identifier: + - value: c63e4630-7bb4-4f01-b9fe-94478000158a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-49d6a6ea-metastasis-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_222_sample_0_subject + identifier: + - value: GENIE-GRCC-49d6a6ea-metastasis-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1f92d968-687e-42bc-a4fc-da0f6c8f6eb9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_223_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_223_diagnosis_0 + identifier: + - value: 562417d9-1094-45a9-9621-7fc5ce203ac3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_223 + identifier: + - value: 4f9fb3f1-243d-49d5-99f4-ad18741a9d7b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD2564 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21871 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_223_sample_0 + identifier: + - value: 4448e3e1-aeff-4ea0-82e4-1692b9b59414 + system: http://crdc.nci.nih.gov/gdc + - value: AD2564_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_223_sample_0_subject + identifier: + - value: AD2564_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4f9fb3f1-243d-49d5-99f4-ad18741a9d7b + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_224_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_224_diagnosis_0 + identifier: + - value: d75594bb-d5e3-496f-b1c9-1743ae942c53 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_224 + identifier: + - value: 5d8c34d4-7cd9-42a8-8a0b-942855493e91 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008027 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_224_sample_0 + identifier: + - value: f0afc508-eff1-4a28-b912-3705a87d607d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008027-5967 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_224_sample_0_subject + identifier: + - value: GENIE-DFCI-008027-5967 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d8c34d4-7cd9-42a8-8a0b-942855493e91 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_225_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_225_diagnosis_0 + identifier: + - value: 366df7ed-b836-4cb0-9146-75d22e0ca019 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_225 + identifier: + - value: af89cebe-213e-4308-91e9-c18af43e0d53 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009836 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_225_sample_0 + identifier: + - value: 356353d1-c8db-4f97-b1d2-0b895cb42266 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009836-7821 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_225_sample_0_subject + identifier: + - value: GENIE-DFCI-009836-7821 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: af89cebe-213e-4308-91e9-c18af43e0d53 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_226_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_226_diagnosis_0 + identifier: + - value: 972c3046-1f6c-40fc-a83a-3b200148a683 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_226 + identifier: + - value: b667a340-8394-4d7c-abf1-377dc01547e8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5830 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24334 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_226_sample_0 + identifier: + - value: ed2a5846-de67-40c3-9074-3adc9edfb0b0 + system: http://crdc.nci.nih.gov/gdc + - value: AD5830_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_226_sample_0_subject + identifier: + - value: AD5830_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b667a340-8394-4d7c-abf1-377dc01547e8 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_227_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_227_diagnosis_0 + identifier: + - value: 0e732992-a174-4861-8e05-a6c3e21107b3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_227 + identifier: + - value: a8b8154f-bf96-4e8a-b7a7-8fe6565d7d18 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001903 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_227_sample_0 + identifier: + - value: ea373411-6d3c-4ee3-b8c1-d79131847aa1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001903-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_227_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001903-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a8b8154f-bf96-4e8a-b7a7-8fe6565d7d18 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_228_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_228_diagnosis_0 + identifier: + - value: 881c2131-1f0d-4b11-8b3a-626918ad5566 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_228 + identifier: + - value: 167f9665-6540-467f-9076-e76235823a53 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0013652 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_228_sample_0 + identifier: + - value: 4c4f2c9b-d2db-42ab-898d-7d6c8c8e4a6e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0013652-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_228_sample_0_subject + identifier: + - value: GENIE-MSK-P-0013652-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 167f9665-6540-467f-9076-e76235823a53 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_229_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_229_diagnosis_0 + identifier: + - value: c1551a30-c8b7-4ba5-b5ed-044b55587a38 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_229 + identifier: + - value: 93f3a536-15a8-436d-91c7-cd0f4d38f01d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003078 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_229_sample_0 + identifier: + - value: 1647be39-e387-4457-a1c0-83483d25ea5e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003078-318 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_229_sample_0_subject + identifier: + - value: GENIE-DFCI-003078-318 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 93f3a536-15a8-436d-91c7-cd0f4d38f01d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_230_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_230_diagnosis_0 + identifier: + - value: 552900c2-144c-4340-aed9-197382fafed4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_230 + identifier: + - value: 4ee4168f-7dcd-4180-bc6e-608b559b6590 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD17916 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19509 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_230_sample_0 + identifier: + - value: d4c804df-7392-4267-908e-8fe8c37d00cd + system: http://crdc.nci.nih.gov/gdc + - value: AD17916_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_230_sample_0_subject + identifier: + - value: AD17916_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4ee4168f-7dcd-4180-bc6e-608b559b6590 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_231_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_231_diagnosis_0 + identifier: + - value: 49e46e5d-46b8-41f2-954e-c3c7b563a55b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_231 + identifier: + - value: 65e5a6fd-3d29-4267-a91f-4934a0dc12b2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-041937 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_231_sample_0 + identifier: + - value: 1108ef37-87b6-4b62-82f3-5e799fc4fb52 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-041937-203493 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_231_sample_0_subject + identifier: + - value: GENIE-DFCI-041937-203493 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 65e5a6fd-3d29-4267-a91f-4934a0dc12b2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_232_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_232_diagnosis_0 + identifier: + - value: cbfef8ff-181a-4048-a571-f78fd34799ef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_232 + identifier: + - value: cba41e7b-05c8-4bff-b2d8-01aefd62506d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037220 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_232_sample_0 + identifier: + - value: 9f95c03c-4c29-47c7-8bff-47c3014a61b5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037220-88689 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_232_sample_0_subject + identifier: + - value: GENIE-DFCI-037220-88689 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cba41e7b-05c8-4bff-b2d8-01aefd62506d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_233_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_233_diagnosis_0 + identifier: + - value: d5b740be-4c9a-4bec-835a-4cd0b394ded4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_233 + identifier: + - value: ec3496ec-672d-4098-a7dd-76c01f83c6ad + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006383 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_233_sample_0 + identifier: + - value: 1a1294ab-79bf-4e29-b958-cd6c3b25a984 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006383-3525 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_233_sample_0_subject + identifier: + - value: GENIE-DFCI-006383-3525 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ec3496ec-672d-4098-a7dd-76c01f83c6ad + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_234_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_234_diagnosis_0 + identifier: + - value: 5c73649d-f112-401e-a47c-785337555930 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_234 + identifier: + - value: 43cf3efc-e6ff-4ae8-b5f2-e029f419cab0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-JHU-02535 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_234_sample_0 + identifier: + - value: d34c6f0f-6b69-4820-8dc8-90d8d54ff7c4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-JHU-02535-03020 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_234_sample_0_subject + identifier: + - value: GENIE-JHU-02535-03020 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 43cf3efc-e6ff-4ae8-b5f2-e029f419cab0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_235_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_235_diagnosis_0 + identifier: + - value: ce0e772c-45e6-4686-9db5-f88e05e2f713 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_235 + identifier: + - value: 6075c870-2f9f-4696-a29c-bd3b5bdd0903 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD12118 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14891 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_235_sample_0 + identifier: + - value: fb315485-9a4d-42a8-8e1b-8cc97c708f1d + system: http://crdc.nci.nih.gov/gdc + - value: AD12118_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_235_sample_0_subject + identifier: + - value: AD12118_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6075c870-2f9f-4696-a29c-bd3b5bdd0903 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_236_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_236_diagnosis_0 + identifier: + - value: 9233f502-9580-4801-915e-732ca0f26a2c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_236 + identifier: + - value: aac14e7b-221c-4987-9f2e-b6a498983286 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-050720 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_236_sample_0 + identifier: + - value: c1353660-3a6c-4a01-8800-d52a40b6ed68 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-050720-203425 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_236_sample_0_subject + identifier: + - value: GENIE-DFCI-050720-203425 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aac14e7b-221c-4987-9f2e-b6a498983286 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_237_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_237_diagnosis_0 + identifier: + - value: 130676ad-54bc-4d20-9ec5-129d4688296d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_237 + identifier: + - value: 1faf4d76-b8f6-4d72-a27f-c86ce27a9f3f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD1478 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14953 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_237_sample_0 + identifier: + - value: 50977953-c3a2-4b71-b40a-3f211a269cc5 + system: http://crdc.nci.nih.gov/gdc + - value: AD1478_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_237_sample_0_subject + identifier: + - value: AD1478_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1faf4d76-b8f6-4d72-a27f-c86ce27a9f3f + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_238_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_238_diagnosis_0 + identifier: + - value: ed6cd70d-8278-4da3-9067-ab74bc051381 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_238 + identifier: + - value: 7499342c-809a-440b-8f11-296840b77e1a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007474 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_238_sample_0 + identifier: + - value: 7946822e-6d72-4013-8be2-f3ffb0487d65 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007474-4132 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_238_sample_0_subject + identifier: + - value: GENIE-DFCI-007474-4132 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7499342c-809a-440b-8f11-296840b77e1a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_239_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_239_diagnosis_0 + identifier: + - value: 247e1e60-27cf-4f37-9a1c-8db3284dcb56 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_239 + identifier: + - value: 33567600-72f8-45fb-8775-ee373f3610f9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008904 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_239_sample_0 + identifier: + - value: 075795d3-4e6e-4edb-95ee-f4d7ca56b337 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008904-6911 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_239_sample_0_subject + identifier: + - value: GENIE-DFCI-008904-6911 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 33567600-72f8-45fb-8775-ee373f3610f9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_240_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_240_diagnosis_0 + identifier: + - value: 3439abcc-0169-490c-8794-73e53b937d7c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_240 + identifier: + - value: c66f00fb-859a-4180-a25e-f09615bb3e39 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037577 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_240_sample_0 + identifier: + - value: 4121fe4a-1ae9-41e4-954d-88c88d047d9c + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037577-74790 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_240_sample_0_subject + identifier: + - value: GENIE-DFCI-037577-74790 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c66f00fb-859a-4180-a25e-f09615bb3e39 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_241_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_241_diagnosis_0 + identifier: + - value: 9eeeccb6-c3a5-4008-a87c-006d2e1efa9f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_241 + identifier: + - value: e8dd87b1-a188-4209-bb3a-436319b22eb0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008672 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_241_sample_0 + identifier: + - value: 6db9d94f-7868-4a64-b9b4-a5b95747c317 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008672-7091 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_241_sample_0_subject + identifier: + - value: GENIE-DFCI-008672-7091 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8dd87b1-a188-4209-bb3a-436319b22eb0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_242_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_242_diagnosis_0 + identifier: + - value: c96ca96a-8046-4381-a767-1119705c5500 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_242 + identifier: + - value: 6ac0f09b-257a-488b-b023-c23b8172f3f3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008037 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_242_sample_0 + identifier: + - value: f5e6b025-48ca-4fd5-b657-ae622bc9de02 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008037-6376 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_242_sample_0_subject + identifier: + - value: GENIE-DFCI-008037-6376 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ac0f09b-257a-488b-b023-c23b8172f3f3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_243_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_243_diagnosis_0 + identifier: + - value: 3adce70b-ce30-4b21-beeb-2a7bda73ca3d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_243 + identifier: + - value: aa289faf-9e8c-4211-96a8-babe95eac89f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008134 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_243_sample_0 + identifier: + - value: 37b86231-4224-4084-a523-800e98c4fea3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008134-5168 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_243_sample_0_subject + identifier: + - value: GENIE-DFCI-008134-5168 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aa289faf-9e8c-4211-96a8-babe95eac89f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_244_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_244_diagnosis_0 + identifier: + - value: f2f2d6b1-7233-433d-b34f-62a8d4e50b0c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_244 + identifier: + - value: 70ff623b-730c-4813-99c5-b02d48e1ce79 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015645 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_244_sample_0 + identifier: + - value: 8a8010f9-2193-4604-9425-da6e5512ebef + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015645-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_244_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015645-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 70ff623b-730c-4813-99c5-b02d48e1ce79 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_245_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_245_diagnosis_0 + identifier: + - value: 45950ba0-9179-4304-9bf7-1a43880d000b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_245 + identifier: + - value: b1feef08-24f3-429b-9b7b-59fce4edc13e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010940 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_245_sample_0 + identifier: + - value: 8642c059-a648-4ced-977f-45d6e6496e7b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010940-9514 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_245_sample_0_subject + identifier: + - value: GENIE-DFCI-010940-9514 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b1feef08-24f3-429b-9b7b-59fce4edc13e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_246_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_246_diagnosis_0 + identifier: + - value: 2e4427b7-e557-49c7-85ef-39a02c4a441c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_246 + identifier: + - value: 26d5f693-dfbc-44ec-a073-49a59a3f09a0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-050738 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_246_sample_0 + identifier: + - value: c6e1507a-83f3-4c51-8275-319d0dcd8f97 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-050738-234120 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_246_sample_0_subject + identifier: + - value: GENIE-DFCI-050738-234120 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 26d5f693-dfbc-44ec-a073-49a59a3f09a0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_247_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_247_diagnosis_0 + identifier: + - value: 9b75ffac-0af8-40a0-9cc6-8472fbe942ef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_247 + identifier: + - value: 46616690-75ad-4cec-bf44-37aa97d96c6f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015763 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_247_sample_0 + identifier: + - value: d02e5c34-3c1e-4a7d-a67d-c2525ac3a734 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015763-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_247_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015763-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 46616690-75ad-4cec-bf44-37aa97d96c6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_248_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_248_diagnosis_0 + identifier: + - value: ce63ab25-f6d3-475c-abca-986d8d91b869 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_248 + identifier: + - value: d71c9c5f-cdfc-4117-8061-19d2ca160054 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0019055 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_248_sample_0 + identifier: + - value: b5793531-8ec1-4bd9-9544-57844ebee0a6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0019055-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_248_sample_0_subject + identifier: + - value: GENIE-MSK-P-0019055-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d71c9c5f-cdfc-4117-8061-19d2ca160054 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_249_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_249_diagnosis_0 + identifier: + - value: 49934fcd-822a-4e1f-ab12-46ef9216779d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_249 + identifier: + - value: 91343a57-cbc3-4b8b-96ab-44057d42ec8c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0009754 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_249_sample_0 + identifier: + - value: 7c2babfc-9948-4332-8c28-096971073c2e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0009754-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_249_sample_0_subject + identifier: + - value: GENIE-MSK-P-0009754-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 91343a57-cbc3-4b8b-96ab-44057d42ec8c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_250_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_250_diagnosis_0 + identifier: + - value: 430602f6-cd8b-48d1-b519-dee691fc9c20 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_250 + identifier: + - value: abc1f3fc-4907-4fd6-a249-917a395a0016 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003106 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_250_sample_0 + identifier: + - value: 78b77808-ec88-4e6b-8393-decaa7bba86d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003106-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_250_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003106-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: abc1f3fc-4907-4fd6-a249-917a395a0016 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_251_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_251_diagnosis_0 + identifier: + - value: 396ba806-81a2-43e2-be95-276cdeee09e3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_251 + identifier: + - value: 57f48c93-043c-4f5b-abb2-76ffa3c46833 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003049 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_251_sample_0 + identifier: + - value: 162d69ba-adac-4884-9d98-3bc70cdb72a7 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003049-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_251_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003049-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 57f48c93-043c-4f5b-abb2-76ffa3c46833 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_252_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_252_diagnosis_0 + identifier: + - value: dabe6d0e-8f19-43d7-9e3d-02a6a24556c8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_252 + identifier: + - value: c8ddaec8-9744-469b-aa42-cd040c97b5fb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002411 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_252_sample_0 + identifier: + - value: e1e98bc8-81b8-45f0-8289-6c306defeaef + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002411-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_252_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002411-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c8ddaec8-9744-469b-aa42-cd040c97b5fb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_253_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_253_diagnosis_0 + identifier: + - value: 80c00d5c-1297-43e4-bbcc-cc895915ec2a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_253 + identifier: + - value: 5d905595-ac94-4363-98a4-0c76bb94843f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-51823bc5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_253_sample_0 + identifier: + - value: 8d24d0d3-ec37-4b8e-9c31-e23965637da9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-51823bc5-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_253_sample_0_subject + identifier: + - value: GENIE-GRCC-51823bc5-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d905595-ac94-4363-98a4-0c76bb94843f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_254_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_254_diagnosis_0 + identifier: + - value: 3f296a63-9ea9-4648-a621-c8fe8a6d631e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_254 + identifier: + - value: 7f70d454-8ac5-40b4-8f29-eeb7d1d2e73f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-cbxznf5u + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_254_sample_0 + identifier: + - value: e0559edf-8fa9-43f1-acbb-7964ea0c33d3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-cbxznf5u-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_254_sample_0_subject + identifier: + - value: GENIE-GRCC-cbxznf5u-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7f70d454-8ac5-40b4-8f29-eeb7d1d2e73f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_255_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_255_diagnosis_0 + identifier: + - value: 05d9d8f7-c21d-47ea-bb12-7de5f6709096 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_255 + identifier: + - value: a30a0b2d-4a44-426b-a8ab-591586e3cac7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD14142 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21690 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_255_sample_0 + identifier: + - value: 02402659-6c66-46ca-861c-e4c093a1a3d3 + system: http://crdc.nci.nih.gov/gdc + - value: AD14142_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_255_sample_0_subject + identifier: + - value: AD14142_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a30a0b2d-4a44-426b-a8ab-591586e3cac7 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_256_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_256_diagnosis_0 + identifier: + - value: 545abbb1-03c0-4b81-af21-3ebb7a5bb299 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_256 + identifier: + - value: 89ffee16-fe0e-4f96-8b0e-281987a2e1bb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD4812 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23191 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_256_sample_0 + identifier: + - value: 4288c5a9-610c-4b1f-b102-2b96b49a6fd8 + system: http://crdc.nci.nih.gov/gdc + - value: AD4812_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_256_sample_0_subject + identifier: + - value: AD4812_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 89ffee16-fe0e-4f96-8b0e-281987a2e1bb + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_257_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_257_diagnosis_0 + identifier: + - value: 96053970-fb5c-4b79-b1bd-8eb8690def1c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_257 + identifier: + - value: 168f7b52-741d-445f-8bcc-e96dcb236b64 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD1118 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 11506 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_257_sample_0 + identifier: + - value: 8f636ed2-41a2-4c3d-bee5-40d9755bf674 + system: http://crdc.nci.nih.gov/gdc + - value: AD1118_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_257_sample_0_subject + identifier: + - value: AD1118_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 168f7b52-741d-445f-8bcc-e96dcb236b64 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_258_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_258_diagnosis_0 + identifier: + - value: cbdf0116-28d4-42a0-ba6e-43a8587de68f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_258 + identifier: + - value: 9c164d1d-1b79-489e-8ed5-3c792c9f3553 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008605 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_258_sample_0 + identifier: + - value: faf18ba4-6d92-4da3-bd43-5071bb88c5e1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008605-9620 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_258_sample_0_subject + identifier: + - value: GENIE-DFCI-008605-9620 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9c164d1d-1b79-489e-8ed5-3c792c9f3553 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_259_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_259_diagnosis_0 + identifier: + - value: 426ed511-e284-4ddd-9809-312805a88905 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_259 + identifier: + - value: b6667b7f-69be-4b81-ac77-7b2941347a5a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD3816 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23030 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_259_sample_0 + identifier: + - value: 3fa16cbf-829f-4097-ac9f-d8016c40c618 + system: http://crdc.nci.nih.gov/gdc + - value: AD3816_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_259_sample_0_subject + identifier: + - value: AD3816_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b6667b7f-69be-4b81-ac77-7b2941347a5a + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_260_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_260_diagnosis_0 + identifier: + - value: fe440219-2351-41cb-a0d1-e22bc73d4aa0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_260 + identifier: + - value: 3cdc53d7-4742-43d4-9b39-36332926875b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD941 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 9352 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_260_sample_0 + identifier: + - value: 5e91c356-4431-478f-8033-99442bcdcb95 + system: http://crdc.nci.nih.gov/gdc + - value: AD941_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_260_sample_0_subject + identifier: + - value: AD941_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3cdc53d7-4742-43d4-9b39-36332926875b + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_261_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_261_diagnosis_0 + identifier: + - value: c58ca3ba-23a8-472b-aab3-94382be12940 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_261 + identifier: + - value: 12b2003d-d51b-4b89-a27e-8a7afc03f704 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010867 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_261_sample_0 + identifier: + - value: d492bfd2-b37d-49c3-a8d5-40171e8442d5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010867-8727 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_261_sample_0_subject + identifier: + - value: GENIE-DFCI-010867-8727 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12b2003d-d51b-4b89-a27e-8a7afc03f704 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_262_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_262_diagnosis_0 + identifier: + - value: 11781aec-74e7-44bc-86ce-9941aa62b6f7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_262 + identifier: + - value: 5d45b0fa-740d-4a73-876d-9948bee401fd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-1594 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_262_sample_0 + identifier: + - value: 4cb8fa37-e3cd-4d7e-bb34-67ffdf228d78 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-1594-3307 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_262_sample_0_subject + identifier: + - value: GENIE-MDA-1594-3307 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d45b0fa-740d-4a73-876d-9948bee401fd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_263_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_263_diagnosis_0 + identifier: + - value: 1c3027a0-7ae3-4ee6-a71d-b357ad841b3c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_263 + identifier: + - value: ec7a1feb-2190-415b-80a8-0840df838253 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD4542 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22230 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Adenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8140/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_263_sample_0 + identifier: + - value: de90601b-1eda-4d1a-aa41-29feebdcfd57 + system: http://crdc.nci.nih.gov/gdc + - value: AD4542_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_263_sample_0_subject + identifier: + - value: AD4542_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ec7a1feb-2190-415b-80a8-0840df838253 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_264_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_264_diagnosis_0 + identifier: + - value: 8bc744c9-1120-41c6-a782-3bda1bbfa2ce + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_264 + identifier: + - value: 57a43a85-7642-48d3-ba74-cd9ff677f9d3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0012578 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_264_sample_0 + identifier: + - value: 31be6816-e615-4939-8c64-c523db6a438e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0012578-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_264_sample_0_subject + identifier: + - value: GENIE-MSK-P-0012578-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 57a43a85-7642-48d3-ba74-cd9ff677f9d3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_265_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_265_diagnosis_0 + identifier: + - value: e68bc170-6152-4c90-9b9b-e31856495716 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_265 + identifier: + - value: 16318d10-9cd1-4de7-9b2e-65e6a608cbe7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0005506 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_265_sample_0 + identifier: + - value: b5f4b393-678a-4964-b625-19c8099cde13 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0005506-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_265_sample_0_subject + identifier: + - value: GENIE-MSK-P-0005506-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 16318d10-9cd1-4de7-9b2e-65e6a608cbe7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_266_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_266_diagnosis_0 + identifier: + - value: 494e7724-f0c8-44b8-a4f9-8e6cc9a2c095 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_266 + identifier: + - value: 3c29272f-6ed7-4be0-9bc0-dbd51f5b3213 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-NKI-FGHG + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_266_sample_0 + identifier: + - value: e91ef1f0-a986-44d2-8880-fbef0afe91d8 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-NKI-FGHG-R6TZ + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_266_sample_0_subject + identifier: + - value: GENIE-NKI-FGHG-R6TZ + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c29272f-6ed7-4be0-9bc0-dbd51f5b3213 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_267_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_267_diagnosis_0 + identifier: + - value: 43aa2337-12ee-410b-9182-0de9352057f0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_267 + identifier: + - value: 9aa4b827-14fc-4ae2-8e90-b2541cf852e6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD3230 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 30260 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_267_sample_0 + identifier: + - value: 900eabba-ab2e-4b0b-9738-db52f9203db9 + system: http://crdc.nci.nih.gov/gdc + - value: AD3230_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_267_sample_0_subject + identifier: + - value: AD3230_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9aa4b827-14fc-4ae2-8e90-b2541cf852e6 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_268_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_268_diagnosis_0 + identifier: + - value: 2ba98ec4-5cc5-43d5-8de3-ab33d0d6779b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_268 + identifier: + - value: f026d5fc-6aaa-4a49-b3be-220838b136f6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003996 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_268_sample_0 + identifier: + - value: 12d6861e-5ad9-48f7-ae61-07c7e45be5a3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003996-1286 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_268_sample_0_subject + identifier: + - value: GENIE-DFCI-003996-1286 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f026d5fc-6aaa-4a49-b3be-220838b136f6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_269_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_269_diagnosis_0 + identifier: + - value: 26bc85c7-5376-467d-a880-4c415ba3b3a5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_269 + identifier: + - value: 99f5659c-bf1b-47ac-8998-2c6d3b3c9a60 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0014015 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_269_sample_0 + identifier: + - value: 968b2133-a7b0-4d2f-8949-f6ff299f1219 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0014015-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_269_sample_0_subject + identifier: + - value: GENIE-MSK-P-0014015-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 99f5659c-bf1b-47ac-8998-2c6d3b3c9a60 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_270_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_270_diagnosis_0 + identifier: + - value: 40d016b6-27a3-4e33-ad6b-f50eaa54e2fa + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_270 + identifier: + - value: 678811da-de50-425a-9806-e839df53b141 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008097 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_270_sample_0 + identifier: + - value: f71f4733-17f4-436f-b12d-bad5b99ceba3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008097-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_270_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008097-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 678811da-de50-425a-9806-e839df53b141 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_271_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_271_diagnosis_0 + identifier: + - value: d2578ad3-da53-4f9a-a3b7-043e9c01a282 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_271 + identifier: + - value: 6ca6d8dc-c963-496f-a4ce-105f1f77645a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD17065 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 10422 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_271_sample_0 + identifier: + - value: c84c230b-7953-4d86-ba93-255ab2242ce7 + system: http://crdc.nci.nih.gov/gdc + - value: AD17065_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_271_sample_0_subject + identifier: + - value: AD17065_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ca6d8dc-c963-496f-a4ce-105f1f77645a + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_272_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_272_diagnosis_0 + identifier: + - value: b0113a66-8202-482a-ad65-dc55cdca3c27 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_272 + identifier: + - value: ac66edd7-551f-4dd5-98dc-7d2b710671c0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD8711 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18941 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_272_sample_0 + identifier: + - value: 3ece7ea7-cad2-4e6d-811f-c91f63a4fca9 + system: http://crdc.nci.nih.gov/gdc + - value: AD8711_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_272_sample_0_subject + identifier: + - value: AD8711_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ac66edd7-551f-4dd5-98dc-7d2b710671c0 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_273_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_273_diagnosis_0 + identifier: + - value: 4228d736-f7fe-4ef9-8bce-39b8c6c3bc70 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_273 + identifier: + - value: dd8d93ad-a82b-4764-8283-423a3c6ce542 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010459 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_273_sample_0 + identifier: + - value: d69183b2-2961-45f3-a4db-3d32d08f6abb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010459-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_273_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010459-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dd8d93ad-a82b-4764-8283-423a3c6ce542 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_274_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_274_diagnosis_0 + identifier: + - value: 4f1912bc-3704-49b0-b916-6d0e99463553 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_274 + identifier: + - value: 6ebfc4ed-b5a2-463c-948f-3c531269f0a8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5075 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 16230 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_274_sample_0 + identifier: + - value: dbf24e2a-1a10-4dfb-be35-8021f82b947c + system: http://crdc.nci.nih.gov/gdc + - value: AD5075_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_274_sample_0_subject + identifier: + - value: AD5075_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ebfc4ed-b5a2-463c-948f-3c531269f0a8 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_275_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_275_diagnosis_0 + identifier: + - value: 59ca6acf-5527-4fa2-8bb2-658029b9c67f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_275 + identifier: + - value: 63d4bf43-6194-46e0-ad9a-bc7934491f74 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009312 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_275_sample_0 + identifier: + - value: 667948dc-d9bd-4813-922b-69468835c551 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009312-6572 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_275_sample_0_subject + identifier: + - value: GENIE-DFCI-009312-6572 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 63d4bf43-6194-46e0-ad9a-bc7934491f74 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_276_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_276_diagnosis_0 + identifier: + - value: d0fdd332-a86e-4d6e-b93f-97937926a834 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_276 + identifier: + - value: cbd0deee-7185-4205-bbc7-8e1bb383b51d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0019630 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_276_sample_0 + identifier: + - value: bbc31a15-3dc6-479c-bd5a-9c1950705ca4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0019630-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_276_sample_0_subject + identifier: + - value: GENIE-MSK-P-0019630-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cbd0deee-7185-4205-bbc7-8e1bb383b51d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_277_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_277_diagnosis_0 + identifier: + - value: 415b0c86-82b5-46c1-b51b-00e701add732 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_277 + identifier: + - value: 8d7e1441-8671-4906-8896-1c27aedc51dc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008675 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_277_sample_0 + identifier: + - value: b1a78f00-1eeb-4c1b-838f-fb8453112c5a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008675-7728 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_277_sample_0_subject + identifier: + - value: GENIE-DFCI-008675-7728 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8d7e1441-8671-4906-8896-1c27aedc51dc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_278_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_278_diagnosis_0 + identifier: + - value: 309da786-ca2c-4c3a-8907-5e690f375f54 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_278 + identifier: + - value: 75421a81-45a5-43b4-ac6f-c739ce863c31 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008800 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_278_sample_0 + identifier: + - value: 5dec4e0d-afbd-4ad6-8acc-00b5ad113a03 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008800-T02-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_278_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008800-T02-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 75421a81-45a5-43b4-ac6f-c739ce863c31 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_279_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_279_diagnosis_0 + identifier: + - value: 6fdb9066-4bcf-42aa-81d1-585b2f2fdaf9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_279 + identifier: + - value: 6afa43bb-cb24-42fb-8236-c736d0d1ed74 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-6209 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_279_sample_0 + identifier: + - value: 0f97f0c0-2148-4c06-97a5-37a64ed1b81d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-6209-17288 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_279_sample_0_subject + identifier: + - value: GENIE-MDA-6209-17288 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6afa43bb-cb24-42fb-8236-c736d0d1ed74 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_280_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_280_diagnosis_0 + identifier: + - value: 215314e4-f8c7-47e1-8993-f126c49bd1a8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_280 + identifier: + - value: 955ebc26-2090-46d9-85b5-5944870063b2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD7896 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18871 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Adenocarcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8140/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_280_sample_0 + identifier: + - value: d3811cf5-8f54-4344-9efc-2f42c49e4e67 + system: http://crdc.nci.nih.gov/gdc + - value: AD7896_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_280_sample_0_subject + identifier: + - value: AD7896_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 955ebc26-2090-46d9-85b5-5944870063b2 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_281_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_281_diagnosis_0 + identifier: + - value: c975f49b-ba03-4e22-bcf1-7aef636601ef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_281 + identifier: + - value: da97eab3-82ed-4b82-8041-6ef46e004c7b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD3546 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15874 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_281_sample_0 + identifier: + - value: 42ef0174-6a5e-4804-ae6e-5d0122cb51c5 + system: http://crdc.nci.nih.gov/gdc + - value: AD3546_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_281_sample_0_subject + identifier: + - value: AD3546_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: da97eab3-82ed-4b82-8041-6ef46e004c7b + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_282_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_282_diagnosis_0 + identifier: + - value: d0d35a5e-572f-4cae-a0df-67ce30803048 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_282 + identifier: + - value: 834d4818-22e3-436e-990e-1d20cab82c0f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD14308 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19073 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_282_sample_0 + identifier: + - value: 32112d7c-2b29-485d-86c3-6b995450ec8c + system: http://crdc.nci.nih.gov/gdc + - value: AD14308_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_282_sample_0_subject + identifier: + - value: AD14308_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 834d4818-22e3-436e-990e-1d20cab82c0f + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_283_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_283_diagnosis_0 + identifier: + - value: 3f8fca8c-e8c8-4032-a0ac-488e49fd623d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_283 + identifier: + - value: 8f820fdc-f3a9-4367-ad66-d548c3eba26d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-023359 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_283_sample_0 + identifier: + - value: 9eb7cb20-106f-4668-9ef4-c0344e8df3c1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-023359-23864 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_283_sample_0_subject + identifier: + - value: GENIE-DFCI-023359-23864 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8f820fdc-f3a9-4367-ad66-d548c3eba26d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_284_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_284_diagnosis_0 + identifier: + - value: 1906d9ae-58dd-4b92-892f-6ff61788d171 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_284 + identifier: + - value: 3604fc5c-f9f7-4be2-89f1-31aef41d836a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005398 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_284_sample_0 + identifier: + - value: adbb22ae-5402-4918-a4d0-b54e2f114253 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005398-2604 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_284_sample_0_subject + identifier: + - value: GENIE-DFCI-005398-2604 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3604fc5c-f9f7-4be2-89f1-31aef41d836a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_285_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_285_diagnosis_0 + identifier: + - value: e978fb2f-2b7c-4ac7-b4c0-fa527f8c4ffb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_285 + identifier: + - value: dacb3f5d-30c1-4e78-a20d-9d7359e5fa80 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-090186 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_285_sample_0 + identifier: + - value: 1bee9751-cbcd-46d2-97ac-bbe9f4495f2c + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-090186-282458 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_285_sample_0_subject + identifier: + - value: GENIE-DFCI-090186-282458 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dacb3f5d-30c1-4e78-a20d-9d7359e5fa80 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_286_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_286_diagnosis_0 + identifier: + - value: aa6e25a1-2d85-423b-a149-8cf11a6947f7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_286 + identifier: + - value: f86214e8-d4fc-4834-b289-081a78c1da55 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010697 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_286_sample_0 + identifier: + - value: 22ef8279-1519-4099-ae13-ff430645c992 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010697-8404 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_286_sample_0_subject + identifier: + - value: GENIE-DFCI-010697-8404 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f86214e8-d4fc-4834-b289-081a78c1da55 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_287_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_287_diagnosis_0 + identifier: + - value: ada2a9ee-43ec-4198-b1e4-bb0c62102973 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_287 + identifier: + - value: 35b9d779-81c4-4c13-8b4c-6b3ec0fbdf98 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003061 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_287_sample_0 + identifier: + - value: 7d368af5-dc58-4ddb-af35-cbc63bd638e4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003061-9096 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_287_sample_0_subject + identifier: + - value: GENIE-DFCI-003061-9096 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 35b9d779-81c4-4c13-8b4c-6b3ec0fbdf98 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_288_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_288_diagnosis_0 + identifier: + - value: a2cd4aae-5655-4082-956c-f5bbc733c576 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_288 + identifier: + - value: a8307f74-1825-44d5-9ad8-f6811ace639a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-UHN-221761 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_288_sample_0 + identifier: + - value: 5103a1f3-d342-462e-9845-9703579d26f8 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-UHN-221761-ARC1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_288_sample_0_subject + identifier: + - value: GENIE-UHN-221761-ARC1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a8307f74-1825-44d5-9ad8-f6811ace639a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_289_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_289_diagnosis_0 + identifier: + - value: c4b50b5a-dee5-481b-8c34-5584abba267f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_289 + identifier: + - value: 380708f9-ca47-4037-94eb-23b731b491cc + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-UHN-614933 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_289_sample_0 + identifier: + - value: 09f9d0e6-10af-4224-a875-8d1e99e90eb5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-UHN-614933-ARC1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_289_sample_0_subject + identifier: + - value: GENIE-UHN-614933-ARC1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 380708f9-ca47-4037-94eb-23b731b491cc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_290_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_290_diagnosis_0 + identifier: + - value: 05282f77-9656-428f-9517-9edc96cb7360 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_290 + identifier: + - value: 27fe814d-5c78-40ea-bfd7-1679c39f53da + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0007543 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_290_sample_0 + identifier: + - value: 025ae6c3-bdbe-4db0-ac71-56df7e80ea0d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0007543-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_290_sample_0_subject + identifier: + - value: GENIE-MSK-P-0007543-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 27fe814d-5c78-40ea-bfd7-1679c39f53da + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_291_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_291_diagnosis_0 + identifier: + - value: 0ab5d8a1-108f-450c-89bd-efd0c4d285ea + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_291 + identifier: + - value: e31df378-4607-414f-b455-8720dc6ed5b3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003059 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_291_sample_0 + identifier: + - value: 1303ddf5-cd55-47c9-9f93-c09d7bbf2f80 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003059-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_291_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003059-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e31df378-4607-414f-b455-8720dc6ed5b3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_292_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_292_diagnosis_0 + identifier: + - value: 60a003d8-42fa-4981-8fa8-a96a6f4205ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_292 + identifier: + - value: 7cf48860-6077-441a-a978-a74535c24651 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0019316 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_292_sample_0 + identifier: + - value: b3eb534b-6441-4294-809a-ab6963d9aa39 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0019316-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_292_sample_0_subject + identifier: + - value: GENIE-MSK-P-0019316-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7cf48860-6077-441a-a978-a74535c24651 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_293_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_293_diagnosis_0 + identifier: + - value: 80571628-74cc-4067-b16e-40cc5b040560 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_293 + identifier: + - value: 598f3650-1d01-4399-80c1-c86585fb14ec + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0020147 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_293_sample_0 + identifier: + - value: 10e9e747-568c-4276-9275-1f1d7cb30f81 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0020147-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_293_sample_0_subject + identifier: + - value: GENIE-MSK-P-0020147-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 598f3650-1d01-4399-80c1-c86585fb14ec + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_294_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_294_diagnosis_0 + identifier: + - value: a00585d3-91dc-4976-87b6-d00c7caf5f5d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_294 + identifier: + - value: 61d627b0-8cdb-4500-8115-0c08c9771f83 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008528 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_294_sample_0 + identifier: + - value: 89fa0392-487d-4839-9c7e-cb82312941c7 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008528-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_294_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008528-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 61d627b0-8cdb-4500-8115-0c08c9771f83 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_295_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_295_diagnosis_0 + identifier: + - value: db8fb969-2213-4290-94de-c3680cd314f7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_295 + identifier: + - value: 9862b6b1-5a0c-4c88-86fb-1013d20e5eec + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD16283 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20394 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_295_sample_0 + identifier: + - value: 0d4e791a-4a50-4c58-a8a5-88e5bf4d7c9c + system: http://crdc.nci.nih.gov/gdc + - value: AD16283_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_295_sample_0_subject + identifier: + - value: AD16283_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9862b6b1-5a0c-4c88-86fb-1013d20e5eec + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_296_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_296_diagnosis_0 + identifier: + - value: e071dcbc-10af-49bd-86cb-b1c8ec549487 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_296 + identifier: + - value: d458c91f-697c-4169-b2cc-e52ab8d78917 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0017414 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_296_sample_0 + identifier: + - value: ff1a3e50-533b-4228-a8fb-93af76ca4b59 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0017414-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_296_sample_0_subject + identifier: + - value: GENIE-MSK-P-0017414-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d458c91f-697c-4169-b2cc-e52ab8d78917 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_297_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_297_diagnosis_0 + identifier: + - value: f50b7ab8-f114-470f-81b0-35ddd9246c46 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_297 + identifier: + - value: 66eb8376-0b60-45e4-9a09-fcac35ecce1e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-034356 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_297_sample_0 + identifier: + - value: 21a0707d-357c-4ea4-aec8-1227b8997cbb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-034356-130499 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_297_sample_0_subject + identifier: + - value: GENIE-DFCI-034356-130499 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 66eb8376-0b60-45e4-9a09-fcac35ecce1e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_298_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_298_diagnosis_0 + identifier: + - value: 601e60c5-25a1-41e7-a47e-2a069cb8e099 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_298 + identifier: + - value: 5c9d56b6-dca0-41c5-ac50-8390b69bda35 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD11228 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 8502 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_298_sample_0 + identifier: + - value: b62623cd-3d81-4e48-bba4-7df880930106 + system: http://crdc.nci.nih.gov/gdc + - value: AD11228_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_298_sample_0_subject + identifier: + - value: AD11228_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5c9d56b6-dca0-41c5-ac50-8390b69bda35 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_299_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_299_diagnosis_0 + identifier: + - value: 533bd04a-5e63-4ae1-a929-487ae3597956 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_299 + identifier: + - value: a0c85ebd-843a-43be-8db6-cbab73db885b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5852 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24221 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_299_sample_0 + identifier: + - value: f7b249aa-b35a-4e08-87b6-e9a79d75edbd + system: http://crdc.nci.nih.gov/gdc + - value: AD5852_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_299_sample_0_subject + identifier: + - value: AD5852_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a0c85ebd-843a-43be-8db6-cbab73db885b + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_300_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_300_diagnosis_0 + identifier: + - value: eaa3ca60-5565-429d-8c4b-a0a6ef7d9fa6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_300 + identifier: + - value: 57a0880c-bb83-47cc-8274-d340cdd8c6ce + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003114 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_300_sample_0 + identifier: + - value: 9e503ae6-5765-4fe6-9a28-eac5a3a93a13 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003114-1605 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_300_sample_0_subject + identifier: + - value: GENIE-DFCI-003114-1605 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 57a0880c-bb83-47cc-8274-d340cdd8c6ce + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_301_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_301_diagnosis_0 + identifier: + - value: 1d93a53e-6030-43c7-b479-9faa6fc8febf + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_301 + identifier: + - value: 7a60f7b0-37df-45a3-a675-7654117825b9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-002633 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_301_sample_0 + identifier: + - value: a8ec3306-0190-4e13-94d1-e269b8479a1d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-002633-5917 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_301_sample_0_subject + identifier: + - value: GENIE-DFCI-002633-5917 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7a60f7b0-37df-45a3-a675-7654117825b9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_302_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_302_diagnosis_0 + identifier: + - value: af6475d1-2529-4772-9e9e-ce83e3dc0cf8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_302 + identifier: + - value: d82c9d69-5cf9-4c69-906a-605462664009 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008645 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_302_sample_0 + identifier: + - value: 30b0ff9c-3106-4ce0-8657-3ed59c1c8fc7 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008645-7086 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_302_sample_0_subject + identifier: + - value: GENIE-DFCI-008645-7086 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d82c9d69-5cf9-4c69-906a-605462664009 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_303_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_303_diagnosis_0 + identifier: + - value: 03f214c1-e688-473f-b84b-5864f56a6a3a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_303 + identifier: + - value: a75a0467-1e35-455f-afb9-1de077f1f015 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-001000 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_303_sample_0 + identifier: + - value: 016681b7-82cb-404f-a175-8cb6d3f6bc62 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-001000-1570 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_303_sample_0_subject + identifier: + - value: GENIE-DFCI-001000-1570 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a75a0467-1e35-455f-afb9-1de077f1f015 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_304_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_304_diagnosis_0 + identifier: + - value: d50387b2-938c-480c-8287-6c8754e06278 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_304 + identifier: + - value: d526382e-7c08-447c-9c73-32deae36764b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-6686 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_304_sample_0 + identifier: + - value: 2022f8c2-108a-4919-bbcf-1dd1ba4fa10b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-6686-17868 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_304_sample_0_subject + identifier: + - value: GENIE-MDA-6686-17868 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d526382e-7c08-447c-9c73-32deae36764b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_305_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_305_diagnosis_0 + identifier: + - value: a1439fe2-31b2-4a31-973f-fbeeb13a965f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_305 + identifier: + - value: cdca91ba-2f4e-4efb-b7f3-1d4d25f66c8c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001405 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_305_sample_0 + identifier: + - value: 5dcad3f6-29d1-4043-8bf8-c8ceb17c5ec4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001405-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_305_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001405-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cdca91ba-2f4e-4efb-b7f3-1d4d25f66c8c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_306_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_306_diagnosis_0 + identifier: + - value: 8a0ce16a-46ec-433a-9679-e76ca74240fc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_306 + identifier: + - value: 2045e9cc-dac8-47f8-9570-ae5abab2a888 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5506 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 16644 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_306_sample_0 + identifier: + - value: 14f00898-8aaa-4008-9eac-0959333c3525 + system: http://crdc.nci.nih.gov/gdc + - value: AD5506_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_306_sample_0_subject + identifier: + - value: AD5506_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2045e9cc-dac8-47f8-9570-ae5abab2a888 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_307_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_307_diagnosis_0 + identifier: + - value: 8b48f2a0-f69b-547c-a9df-35b18ec7bb5a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_307 + identifier: + - value: 22233a31-023f-412f-9b42-73b58c51dee8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A63U + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18272 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_307_sample_0 + identifier: + - value: a6af965f-ae37-421d-98d6-a69ce62213ac + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63U-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_307_sample_0_subject + identifier: + - value: TCGA-CN-A63U-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22233a31-023f-412f-9b42-73b58c51dee8 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 504 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_307_sample_1 + identifier: + - value: 812b8ee1-096a-40ff-914d-9957644b7d11 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63U-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_307_sample_1_subject + identifier: + - value: TCGA-CN-A63U-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22233a31-023f-412f-9b42-73b58c51dee8 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 504 + unit: + coding: *id001 + quantity_collected: + value_decimal: 200 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_307_sample_2 + identifier: + - value: b4430e0f-983c-454d-926e-a33fcb4cd02c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63U-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_307_sample_2_subject + identifier: + - value: TCGA-CN-A63U-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22233a31-023f-412f-9b42-73b58c51dee8 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_308_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_308_diagnosis_0 + identifier: + - value: 5a687c66-0c8c-5e23-bd7c-6988abb14d66 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_308 + identifier: + - value: 9eb1997f-14f5-4230-ae4f-1ef1943e1723 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6021 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23212 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_308_sample_0 + identifier: + - value: 619a1a7c-f360-4e07-aa85-812e2b1bd92f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6021-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_308_sample_0_subject + identifier: + - value: TCGA-CN-6021-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9eb1997f-14f5-4230-ae4f-1ef1943e1723 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_308_sample_1 + identifier: + - value: f1cbf326-7657-4c9b-9c8d-e2036e89fd07 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6021-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_308_sample_1_subject + identifier: + - value: TCGA-CN-6021-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9eb1997f-14f5-4230-ae4f-1ef1943e1723 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_308_sample_2 + identifier: + - value: edcbcb1d-23bb-4177-8f77-71071822cd89 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6021-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_308_sample_2_subject + identifier: + - value: TCGA-CN-6021-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9eb1997f-14f5-4230-ae4f-1ef1943e1723 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_309_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_309_diagnosis_0 + identifier: + - value: fc136a78-0ba0-5a79-a4f9-d5d692e61222 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_309 + identifier: + - value: 91e30123-2265-4cf1-8389-f6462897837c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7402 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25138 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_309_sample_0 + identifier: + - value: b86e8a21-6937-4299-89f6-05f51888f5d8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7402-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_309_sample_0_subject + identifier: + - value: TCGA-CR-7402-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 91e30123-2265-4cf1-8389-f6462897837c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_309_sample_1 + identifier: + - value: dfdf096f-9577-4e8f-8e98-9b808e417ccc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7402-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_309_sample_1_subject + identifier: + - value: TCGA-CR-7402-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 91e30123-2265-4cf1-8389-f6462897837c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_310_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_310_diagnosis_0 + identifier: + - value: 09ac3334-b77e-56e2-a46b-57faf703f1fb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_310 + identifier: + - value: 9f89510c-ed07-471f-b35e-7c87c237b9fe + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7385 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15477 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_310_sample_0 + identifier: + - value: 4c4a6867-babe-4032-a639-a9b31cdddc6c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7385-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_310_sample_0_subject + identifier: + - value: TCGA-CR-7385-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9f89510c-ed07-471f-b35e-7c87c237b9fe + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_310_sample_1 + identifier: + - value: d1553b1a-bc1e-4dcf-a273-b3effabe380b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7385-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_310_sample_1_subject + identifier: + - value: TCGA-CR-7385-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9f89510c-ed07-471f-b35e-7c87c237b9fe + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_311_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_311_diagnosis_0 + identifier: + - value: 3896106f-2770-565a-b872-0d61198bb107 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_311 + identifier: + - value: 3c975b68-4a6e-4c97-a8d1-b9a427d4957c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5442 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 28040 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2004-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C05.0 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_311_sample_0 + identifier: + - value: 26243d14-e401-4ca4-92e7-aee13c9e6e47 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5442-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_311_sample_0_subject + identifier: + - value: TCGA-CV-5442-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c975b68-4a6e-4c97-a8d1-b9a427d4957c + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_311_sample_1 + identifier: + - value: 698208bb-7272-4ad5-9cc0-909cb669bdaf + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5442-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_311_sample_1_subject + identifier: + - value: TCGA-CV-5442-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c975b68-4a6e-4c97-a8d1-b9a427d4957c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_311_sample_2 + identifier: + - value: ec885af4-3513-4790-ab1f-6ecc94b6115d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5442-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_311_sample_2_subject + identifier: + - value: TCGA-CV-5442-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3c975b68-4a6e-4c97-a8d1-b9a427d4957c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_312_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_312_diagnosis_0 + identifier: + - value: d4b70019-403e-5a16-b7aa-5ed71d54a517 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_312 + identifier: + - value: e8b0a499-7e9a-4f0e-b552-8e4f284141ed + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6473 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24857 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_312_sample_0 + identifier: + - value: ed96ee9b-cf03-4eaa-b783-07b739e3a648 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6473-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_312_sample_0_subject + identifier: + - value: TCGA-CR-6473-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8b0a499-7e9a-4f0e-b552-8e4f284141ed + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_312_sample_1 + identifier: + - value: a9e7990e-7daa-4c79-a836-ac1ad63aaa37 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6473-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_312_sample_1_subject + identifier: + - value: TCGA-CR-6473-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8b0a499-7e9a-4f0e-b552-8e4f284141ed + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_313_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_313_diagnosis_0 + identifier: + - value: 4679b4bd-c891-5a60-9b12-1e6bf1bb7675 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_313 + identifier: + - value: 28d2fd8e-abe9-4ea3-87e4-4f2b61a33c90 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A4IF + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21635 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.3 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_313_sample_0 + identifier: + - value: 5eea7c58-96b4-426b-9685-15599e534730 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4IF-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_313_sample_0_subject + identifier: + - value: TCGA-BA-A4IF-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 28d2fd8e-abe9-4ea3-87e4-4f2b61a33c90 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 483 + unit: + coding: *id001 + quantity_collected: + value_decimal: 170 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_313_sample_1 + identifier: + - value: 7bfdae74-2bf4-4ec7-b08c-acd9b9e0baf4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4IF-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_313_sample_1_subject + identifier: + - value: TCGA-BA-A4IF-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 28d2fd8e-abe9-4ea3-87e4-4f2b61a33c90 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 559 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_314_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_314_diagnosis_0 + identifier: + - value: cdd012e7-6539-5ffe-a4b7-b36a6233b1ec + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_314 + identifier: + - value: 0de19185-3517-4e30-925b-7eb1f5079ec2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A6DJ + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22967 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_314_sample_0 + identifier: + - value: 4210ffee-2a83-4f05-8935-2687503c83d4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DJ-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_314_sample_0_subject + identifier: + - value: TCGA-BA-A6DJ-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0de19185-3517-4e30-925b-7eb1f5079ec2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 388 + unit: + coding: *id001 + quantity_collected: + value_decimal: 360 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_314_sample_1 + identifier: + - value: bbee89dc-6858-45c3-a9fc-c455851f96a8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DJ-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_314_sample_1_subject + identifier: + - value: TCGA-BA-A6DJ-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0de19185-3517-4e30-925b-7eb1f5079ec2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 388 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_314_sample_2 + identifier: + - value: 735334b4-6c30-4a7a-aa54-63f506b8e2bb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DJ-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_314_sample_2_subject + identifier: + - value: TCGA-BA-A6DJ-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0de19185-3517-4e30-925b-7eb1f5079ec2 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_315_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_315_diagnosis_0 + identifier: + - value: 12b8aa2a-5f0f-4d64-9cc0-ff4a65619c10 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_315 + identifier: + - value: 513cac3d-7120-4a12-bab8-50647e106b8c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003438 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_315_sample_0 + identifier: + - value: 8ccd1ad3-a277-468d-ae44-03e6c1964c3d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003438-7875 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_315_sample_0_subject + identifier: + - value: GENIE-DFCI-003438-7875 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 513cac3d-7120-4a12-bab8-50647e106b8c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_316_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_316_diagnosis_0 + identifier: + - value: ea9b7e18-cbc5-4588-8b59-d32af85db2c0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_316 + identifier: + - value: 0e04c4fb-d7e4-48eb-83a1-c2a0c47002b7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-052774 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_316_sample_0 + identifier: + - value: f37609a0-84b8-4203-9497-9f60cc8be539 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-052774-173461 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_316_sample_0_subject + identifier: + - value: GENIE-DFCI-052774-173461 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0e04c4fb-d7e4-48eb-83a1-c2a0c47002b7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_317_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_317_diagnosis_0 + identifier: + - value: d2a0bb97-195f-422a-969f-0342485cf8c6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_317 + identifier: + - value: 6cddf78c-c273-4545-b3cb-ce317911822a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010743 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_317_sample_0 + identifier: + - value: 1f6b16e8-e1f4-462a-ac25-700c915f464f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010743-8938 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_317_sample_0_subject + identifier: + - value: GENIE-DFCI-010743-8938 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6cddf78c-c273-4545-b3cb-ce317911822a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_318_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_318_diagnosis_0 + identifier: + - value: d68e9ec8-d562-49e0-abf1-ebc41a0f439a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_318 + identifier: + - value: 7d9c12bb-fbef-4a8c-ada2-9015fbf40fec + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006509 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_318_sample_0 + identifier: + - value: 3e441a98-f869-414d-9732-4b4037711d5e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006509-3496 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_318_sample_0_subject + identifier: + - value: GENIE-DFCI-006509-3496 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7d9c12bb-fbef-4a8c-ada2-9015fbf40fec + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_319_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_319_diagnosis_0 + identifier: + - value: 37ac68db-02ec-42d2-92bc-d7d2f4c33bf8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_319 + identifier: + - value: 4f61e323-cd86-4bd4-b892-a0f95ec8fd55 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008078 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_319_sample_0 + identifier: + - value: f2c471a5-55a3-4180-be7d-c3560efade4b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008078-6166 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_319_sample_0_subject + identifier: + - value: GENIE-DFCI-008078-6166 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4f61e323-cd86-4bd4-b892-a0f95ec8fd55 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_320_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_320_diagnosis_0 + identifier: + - value: f0b5d732-2466-4d9a-90cb-ec3084606849 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_320 + identifier: + - value: c51cfd96-0eae-45e9-b5b2-a0f30d328144 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010677 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_320_sample_0 + identifier: + - value: e084b5e5-05ac-4229-bbe8-f640f231e1fb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010677-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_320_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010677-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c51cfd96-0eae-45e9-b5b2-a0f30d328144 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_321_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_321_diagnosis_0 + identifier: + - value: 8932404c-6adc-4b1d-81fb-fdb4dbb32ddd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_321 + identifier: + - value: ae951300-7a00-4651-b3e2-afa541341987 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008185 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_321_sample_0 + identifier: + - value: 3a9e0ea1-fb4f-47bd-bf6c-831f7101b005 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008185-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_321_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008185-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ae951300-7a00-4651-b3e2-afa541341987 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_322_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_322_diagnosis_0 + identifier: + - value: e2403080-b7b5-4d13-b62e-9b7293a45058 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_322 + identifier: + - value: d9904f53-5783-4424-a900-0a03d4f40b72 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002484 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_322_sample_0 + identifier: + - value: 89363cf2-b8d0-48cd-97e5-4cd68ed372d3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002484-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_322_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002484-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d9904f53-5783-4424-a900-0a03d4f40b72 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_323_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_323_diagnosis_0 + identifier: + - value: 27b201c5-0310-4f7a-835c-31fde311cde6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_323 + identifier: + - value: 910f2077-10f3-4c4f-825c-38068158201e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0020040 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_323_sample_0 + identifier: + - value: 8738d7cc-e80c-4a00-bc4e-fee451f4b19f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0020040-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_323_sample_0_subject + identifier: + - value: GENIE-MSK-P-0020040-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 910f2077-10f3-4c4f-825c-38068158201e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_324_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_324_diagnosis_0 + identifier: + - value: 6c55b480-1444-4ae1-a079-72287e8794a4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_324 + identifier: + - value: d13be96b-fd31-41e9-a997-85f7d0b9d68b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0017687 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_324_sample_0 + identifier: + - value: 52f200af-cd9b-4d63-91fc-7bf44c67c537 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0017687-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_324_sample_0_subject + identifier: + - value: GENIE-MSK-P-0017687-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d13be96b-fd31-41e9-a997-85f7d0b9d68b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_325_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_325_diagnosis_0 + identifier: + - value: 68a8cfd1-e890-4bd7-931b-33636e8cf10b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_325 + identifier: + - value: f8b0618b-90dd-4948-b1cc-06a6f8464054 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000668 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_325_sample_0 + identifier: + - value: 5c9ff077-5620-4611-a58c-fdd8ed98b2db + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000668-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_325_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000668-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f8b0618b-90dd-4948-b1cc-06a6f8464054 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_326_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_326_diagnosis_0 + identifier: + - value: 6f840d0f-a369-413c-baf1-35200313c274 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_326 + identifier: + - value: 782db87d-65cf-439d-a74f-bde38aec0652 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-a679ee35 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_326_sample_0 + identifier: + - value: 60e15dc9-5d8b-4104-b6c3-bc0b7b3109a5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-a679ee35-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_326_sample_0_subject + identifier: + - value: GENIE-GRCC-a679ee35-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 782db87d-65cf-439d-a74f-bde38aec0652 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_327_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_327_diagnosis_0 + identifier: + - value: 675831ed-0976-4fdb-87da-15a7a85ba6b5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_327 + identifier: + - value: a579c6ea-ffdf-42d3-8a91-0fb082a58a15 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-9bb5e551 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_327_sample_0 + identifier: + - value: b2ee3f62-a9d8-4f49-bc51-1d3f17d63b14 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-9bb5e551-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_327_sample_0_subject + identifier: + - value: GENIE-GRCC-9bb5e551-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a579c6ea-ffdf-42d3-8a91-0fb082a58a15 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_328_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_328_diagnosis_0 + identifier: + - value: 1137ba9a-12d3-4b2d-a3a4-d95de8bcf49a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_328 + identifier: + - value: 6c1e535b-7ca4-4727-b514-ac62953c598c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-8191e4ea + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_328_sample_0 + identifier: + - value: 783e6c97-20aa-4c8b-a7e1-ae0d8f7af28d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-8191e4ea-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_328_sample_0_subject + identifier: + - value: GENIE-GRCC-8191e4ea-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6c1e535b-7ca4-4727-b514-ac62953c598c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_329_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_329_diagnosis_0 + identifier: + - value: 52fd0265-204c-4ce3-bb51-a3cbee5aca51 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_329 + identifier: + - value: ad8ff874-4117-4c42-b110-be13ca5cefa7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-115ef99e + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_329_sample_0 + identifier: + - value: 6ba7ff9a-775d-4239-884f-4a303b42e4fd + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-115ef99e-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_329_sample_0_subject + identifier: + - value: GENIE-GRCC-115ef99e-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ad8ff874-4117-4c42-b110-be13ca5cefa7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_330_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_330_diagnosis_0 + identifier: + - value: cf507905-7cf2-408b-a08e-b703df54147f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_330 + identifier: + - value: 037d94c6-b26e-463b-9786-d880656cb6d9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-NKI-DYRQ + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_330_sample_0 + identifier: + - value: 36b762ea-ade4-4e7a-b824-0fdadd0e33ef + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-NKI-DYRQ-CX3U + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_330_sample_0_subject + identifier: + - value: GENIE-NKI-DYRQ-CX3U + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 037d94c6-b26e-463b-9786-d880656cb6d9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_331_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_331_diagnosis_0 + identifier: + - value: 3d039654-a9ad-4641-b459-bd7ccd1ec1b6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_331 + identifier: + - value: 63abf18d-e0fe-42c0-97cb-01a610fc4c8c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-NKI-MCU4 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_331_sample_0 + identifier: + - value: b34b2488-73cb-480c-a1ac-c2ef5b89c5f0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-NKI-MCU4-LAZM + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_331_sample_0_subject + identifier: + - value: GENIE-NKI-MCU4-LAZM + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 63abf18d-e0fe-42c0-97cb-01a610fc4c8c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_332_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_332_diagnosis_0 + identifier: + - value: 4fdd25bc-4056-47f1-8eb9-7e572313ba5d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_332 + identifier: + - value: 06fe239f-43a5-44b1-8c9f-771eb98bbf44 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009927 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_332_sample_0 + identifier: + - value: c65b0cad-f2f5-40f2-a523-60374faf390a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009927-9027 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_332_sample_0_subject + identifier: + - value: GENIE-DFCI-009927-9027 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 06fe239f-43a5-44b1-8c9f-771eb98bbf44 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_333_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_333_diagnosis_0 + identifier: + - value: e1518a49-5ef2-41ca-ac88-edc88e8ec241 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_333 + identifier: + - value: 368dc1be-66c0-4913-ad69-79f4ae715f47 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-e8aa0080 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_333_sample_0 + identifier: + - value: baf6aa81-4b32-4d7f-8557-5942a0febb91 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-e8aa0080-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_333_sample_0_subject + identifier: + - value: GENIE-GRCC-e8aa0080-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 368dc1be-66c0-4913-ad69-79f4ae715f47 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_334_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_334_diagnosis_0 + identifier: + - value: 6579daca-0ec7-49e8-92e5-6a6b7c379b8d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_334 + identifier: + - value: fe6fa49b-ae91-40a8-a85e-df13563fb38a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-h39utsgs + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_334_sample_0 + identifier: + - value: 1f1c82de-2931-4f38-9caf-213d5425ded1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-h39utsgs-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_334_sample_0_subject + identifier: + - value: GENIE-GRCC-h39utsgs-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fe6fa49b-ae91-40a8-a85e-df13563fb38a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_335_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_335_diagnosis_0 + identifier: + - value: 00fbc722-7387-437d-b859-3d35c86e02fc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_335 + identifier: + - value: 9f1965ba-c8ce-4886-a71b-57d06cc71369 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-040b2fef + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_335_sample_0 + identifier: + - value: 25007740-c3ea-41f0-a9dc-52de44cb9faa + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-040b2fef-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_335_sample_0_subject + identifier: + - value: GENIE-GRCC-040b2fef-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9f1965ba-c8ce-4886-a71b-57d06cc71369 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_336_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_336_diagnosis_0 + identifier: + - value: 770f08b4-6ea7-4cb0-a423-75909447e60c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_336 + identifier: + - value: e1e1c82f-3cfe-4f7d-a6cb-8a093e2dada9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-518360 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_336_sample_0 + identifier: + - value: 75fdf08c-00e0-42dd-a21c-62cceb7bf00f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-518360-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_336_sample_0_subject + identifier: + - value: GENIE-VICC-518360-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e1e1c82f-3cfe-4f7d-a6cb-8a093e2dada9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_337_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_337_diagnosis_0 + identifier: + - value: 4e9b9fad-2d73-4867-b7f8-8e42769ea41e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_337 + identifier: + - value: 2f0aadcb-1b81-4643-95fd-4374198db175 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-009088 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_337_sample_0 + identifier: + - value: cc6054a8-ec09-42af-be24-4041b7be75cc + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-009088-5942 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_337_sample_0_subject + identifier: + - value: GENIE-DFCI-009088-5942 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2f0aadcb-1b81-4643-95fd-4374198db175 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_338_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_338_diagnosis_0 + identifier: + - value: 49cde226-3d69-415f-ad98-02d190dbf75c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_338 + identifier: + - value: ee0395cc-3774-42c7-996d-c64d300c3983 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-006446 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_338_sample_0 + identifier: + - value: 5c19b5fa-d6eb-4d7e-b617-930e19aea484 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-006446-3455 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_338_sample_0_subject + identifier: + - value: GENIE-DFCI-006446-3455 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ee0395cc-3774-42c7-996d-c64d300c3983 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_339_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_339_diagnosis_0 + identifier: + - value: 0ea10d4e-1809-4763-b440-8e077ecab3e5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_339 + identifier: + - value: 7d1f13c4-bd21-44ef-88ab-91c5f844bdd1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD17629 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 16191 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_339_sample_0 + identifier: + - value: 9ab974e3-bc94-4f83-b7dc-82285f5b4b69 + system: http://crdc.nci.nih.gov/gdc + - value: AD17629_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_339_sample_0_subject + identifier: + - value: AD17629_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7d1f13c4-bd21-44ef-88ab-91c5f844bdd1 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_340_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_340_diagnosis_0 + identifier: + - value: 0cf011bf-054a-4eea-aacc-b963ff83734a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_340 + identifier: + - value: 9399213f-2fa0-4935-8c34-e7e92a526f95 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007960 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_340_sample_0 + identifier: + - value: c353a3fb-dad8-4a6c-acd3-4121eb21b98e + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007960-5976 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_340_sample_0_subject + identifier: + - value: GENIE-DFCI-007960-5976 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9399213f-2fa0-4935-8c34-e7e92a526f95 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_341_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_341_diagnosis_0 + identifier: + - value: 35adcfa2-f4ae-4aec-8362-097fab231545 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_341 + identifier: + - value: 9ff269a7-d7ed-49e4-b6e6-6f8ae88ec30a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-000205 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_341_sample_0 + identifier: + - value: ab00664b-8f6a-493d-b000-89f1341dc713 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-000205-461 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_341_sample_0_subject + identifier: + - value: GENIE-DFCI-000205-461 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9ff269a7-d7ed-49e4-b6e6-6f8ae88ec30a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_342_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_342_diagnosis_0 + identifier: + - value: acb41bec-39c8-477f-8cc2-b8c982bf5b2a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_342 + identifier: + - value: af2edf25-d8c4-4194-9cb0-0628f5c752b3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD9755 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19500 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_342_sample_0 + identifier: + - value: 2b14983f-b848-45de-9881-5dc4f483f7a4 + system: http://crdc.nci.nih.gov/gdc + - value: AD9755_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_342_sample_0_subject + identifier: + - value: AD9755_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: af2edf25-d8c4-4194-9cb0-0628f5c752b3 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_343_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_343_diagnosis_0 + identifier: + - value: c1111640-7729-436a-9b46-88c0ab534b96 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_343 + identifier: + - value: 58a93f49-9787-4bbb-921d-35b2dd4cb08f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-832679ee + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_343_sample_0 + identifier: + - value: 9590434b-5b17-4ee8-b109-7ebb737252ef + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-832679ee-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_343_sample_0_subject + identifier: + - value: GENIE-GRCC-832679ee-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 58a93f49-9787-4bbb-921d-35b2dd4cb08f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_344_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_344_diagnosis_0 + identifier: + - value: 23193585-2a17-41cb-b577-8044058658ea + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_344 + identifier: + - value: 30ecad98-02be-4b40-b178-deb7476b934b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-8k5ygy35 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_344_sample_0 + identifier: + - value: 5db1c5e8-ddbb-4057-a059-6acf46826258 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-8k5ygy35-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_344_sample_0_subject + identifier: + - value: GENIE-GRCC-8k5ygy35-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 30ecad98-02be-4b40-b178-deb7476b934b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_345_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_345_diagnosis_0 + identifier: + - value: 664c73af-7fd8-43bf-9a1c-1109c71a303a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_345 + identifier: + - value: 1d9cac95-ddb5-41e2-a9ad-3e2005132331 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-6a5b9e32 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_345_sample_0 + identifier: + - value: e6616639-64a7-4462-9676-1b2420f371d6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-6a5b9e32-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_345_sample_0_subject + identifier: + - value: GENIE-GRCC-6a5b9e32-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1d9cac95-ddb5-41e2-a9ad-3e2005132331 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_346_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_346_diagnosis_0 + identifier: + - value: 576b4319-20fe-4dd8-82b1-c34a70bd2182 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_346 + identifier: + - value: acdcb34c-aed8-470a-aac7-4c02134bd6b4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-596e5ce8 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_346_sample_0 + identifier: + - value: 7889cf51-be9b-4193-b057-5f348fca10db + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-596e5ce8-metastasis-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_346_sample_0_subject + identifier: + - value: GENIE-GRCC-596e5ce8-metastasis-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: acdcb34c-aed8-470a-aac7-4c02134bd6b4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_347_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_347_diagnosis_0 + identifier: + - value: be59114f-e2eb-4d06-824e-7aa867673eda + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_347 + identifier: + - value: 4fb70d09-7c9f-43c7-817c-076ac5d5c9c7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004755 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_347_sample_0 + identifier: + - value: 255bbe44-dce0-4905-86bb-317144348172 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004755-1862 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_347_sample_0_subject + identifier: + - value: GENIE-DFCI-004755-1862 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4fb70d09-7c9f-43c7-817c-076ac5d5c9c7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_348_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_348_diagnosis_0 + identifier: + - value: 0be93ffc-ad62-42bb-892a-ba10c4da6f39 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_348 + identifier: + - value: 5eddc31c-b9b8-4cf2-a0d7-a4134b79a610 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0017332 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_348_sample_0 + identifier: + - value: 43637316-5d63-491d-b4cd-2caa045d8c7d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0017332-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_348_sample_0_subject + identifier: + - value: GENIE-MSK-P-0017332-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5eddc31c-b9b8-4cf2-a0d7-a4134b79a610 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_349_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_349_diagnosis_0 + identifier: + - value: bcef8cad-3d18-4cd2-b839-5fddd16311f1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_349 + identifier: + - value: 6ecb3d82-8d4c-443e-bfaa-36bbf1801f7d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000945 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_349_sample_0 + identifier: + - value: 2ba57cf3-fd06-4f99-9ad7-447a164b9586 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000945-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_349_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000945-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ecb3d82-8d4c-443e-bfaa-36bbf1801f7d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_350_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_350_diagnosis_0 + identifier: + - value: 0501e7a7-232b-58be-9425-92f1ccd697a4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_350 + identifier: + - value: 12d05e8f-8d13-47c1-b713-2250f6abcef9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4727 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20748 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_350_sample_0 + identifier: + - value: cc2d6cfa-7640-44dd-a200-68fd9f9ee69c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4727-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_350_sample_0_subject + identifier: + - value: TCGA-CN-4727-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12d05e8f-8d13-47c1-b713-2250f6abcef9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_350_sample_1 + identifier: + - value: f102aef0-94b8-4d26-8055-35b76da9dd5f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4727-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_350_sample_1_subject + identifier: + - value: TCGA-CN-4727-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12d05e8f-8d13-47c1-b713-2250f6abcef9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_350_sample_2 + identifier: + - value: a7257360-c4dd-4f59-bfb9-c8d593050146 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4727-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_350_sample_2_subject + identifier: + - value: TCGA-CN-4727-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12d05e8f-8d13-47c1-b713-2250f6abcef9 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_351_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_351_diagnosis_0 + identifier: + - value: ea23b8a9-c2fd-5392-8625-a26662cdf0ef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_351 + identifier: + - value: d189a6c6-210f-4957-b500-457d5ce3f867 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7404 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19532 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_351_sample_0 + identifier: + - value: a39131b9-e7c7-4385-a1b9-d8a0a0950337 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7404-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_351_sample_0_subject + identifier: + - value: TCGA-CR-7404-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d189a6c6-210f-4957-b500-457d5ce3f867 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_351_sample_1 + identifier: + - value: a0723862-62f9-4770-b415-e8f52c447e7a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7404-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_351_sample_1_subject + identifier: + - value: TCGA-CR-7404-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d189a6c6-210f-4957-b500-457d5ce3f867 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_352_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_352_diagnosis_0 + identifier: + - value: fb148e0b-2d1c-57ff-acd6-4f2208af3ce3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_352 + identifier: + - value: bd75d8ee-916b-4abc-bf33-bce6a4217076 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A4IH + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21094 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Basaloid squamous cell carcinoma + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8083/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_352_sample_0 + identifier: + - value: eff60f0d-e3c1-4a93-9026-c0764c70ba9f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4IH-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_352_sample_0_subject + identifier: + - value: TCGA-BA-A4IH-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: bd75d8ee-916b-4abc-bf33-bce6a4217076 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 173 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_352_sample_1 + identifier: + - value: f87efb5e-24f5-4d2b-b6b3-987bbda30e03 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4IH-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_352_sample_1_subject + identifier: + - value: TCGA-BA-A4IH-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: bd75d8ee-916b-4abc-bf33-bce6a4217076 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 97 + unit: + coding: *id001 + quantity_collected: + value_decimal: 380 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_353_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_353_diagnosis_0 + identifier: + - value: c127a1e6-f25a-525b-949d-013bac98b38a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_353 + identifier: + - value: e95e9e7d-a1ed-46eb-9cf8-1d355bf0577f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-DQ-5629 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23550 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_353_sample_0 + identifier: + - value: 769f3c1c-323e-4f04-9ae7-e41f484a964c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-5629-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_353_sample_0_subject + identifier: + - value: TCGA-DQ-5629-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e95e9e7d-a1ed-46eb-9cf8-1d355bf0577f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_353_sample_1 + identifier: + - value: cb2da33c-021a-4af5-8509-118bc1e8e0d5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-5629-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_353_sample_1_subject + identifier: + - value: TCGA-DQ-5629-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e95e9e7d-a1ed-46eb-9cf8-1d355bf0577f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_353_sample_2 + identifier: + - value: 57ea3eed-f8e2-4310-90c0-50d89f818a12 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-5629-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_353_sample_2_subject + identifier: + - value: TCGA-DQ-5629-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e95e9e7d-a1ed-46eb-9cf8-1d355bf0577f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_354_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_354_diagnosis_0 + identifier: + - value: c239680c-7353-50f5-a155-33973562e904 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_354 + identifier: + - value: 2d74e19e-9677-491f-b9ea-4874db64747a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A45W + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27743 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 5th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_354_sample_0 + identifier: + - value: 7202ca4b-6caf-4f4d-adc9-4c59b00cbdc3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45W-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_354_sample_0_subject + identifier: + - value: TCGA-CV-A45W-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2d74e19e-9677-491f-b9ea-4874db64747a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4786 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_354_sample_1 + identifier: + - value: f9ae08e7-9166-4699-801a-4bed11f72dc2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45W-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_354_sample_1_subject + identifier: + - value: TCGA-CV-A45W-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2d74e19e-9677-491f-b9ea-4874db64747a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4786 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_354_sample_2 + identifier: + - value: fe66156a-b3ea-4ed1-a5ca-68a3664c3505 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45W-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_354_sample_2_subject + identifier: + - value: TCGA-CV-A45W-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2d74e19e-9677-491f-b9ea-4874db64747a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_355_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_355_diagnosis_0 + identifier: + - value: 24058118-f7b3-53d4-b24b-07a2ac2e66b1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_355 + identifier: + - value: b98867d7-7d5a-4c58-8878-37bee6f2f4fa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5369 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 32871 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C05.0 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_355_sample_0 + identifier: + - value: 8d31f35c-9178-447d-9a2b-acc305fab407 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5369-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_355_sample_0_subject + identifier: + - value: TCGA-CN-5369-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b98867d7-7d5a-4c58-8878-37bee6f2f4fa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_355_sample_1 + identifier: + - value: b4c02606-0f86-46e4-9daf-dc7dbcd60d78 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5369-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_355_sample_1_subject + identifier: + - value: TCGA-CN-5369-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b98867d7-7d5a-4c58-8878-37bee6f2f4fa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_355_sample_2 + identifier: + - value: 11d697ec-f451-4102-a908-e44f48ab0800 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5369-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_355_sample_2_subject + identifier: + - value: TCGA-CN-5369-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b98867d7-7d5a-4c58-8878-37bee6f2f4fa + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_356_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_356_diagnosis_0 + identifier: + - value: 64881717-bcb2-532a-b0af-395ba5c62c2e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_356 + identifier: + - value: 9a76bd98-1d2b-4d0f-9772-883520ff6210 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6481 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17203 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_356_sample_0 + identifier: + - value: e9a39a90-6401-4a9f-baa5-606e8b5176f6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6481-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_356_sample_0_subject + identifier: + - value: TCGA-CR-6481-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9a76bd98-1d2b-4d0f-9772-883520ff6210 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_356_sample_1 + identifier: + - value: 04652163-a674-446f-9e86-607de19e4c34 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6481-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_356_sample_1_subject + identifier: + - value: TCGA-CR-6481-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9a76bd98-1d2b-4d0f-9772-883520ff6210 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_357_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_357_diagnosis_0 + identifier: + - value: 1214a9ed-2d43-50a7-9a94-85eaa002670b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_357 + identifier: + - value: 17885905-280f-40fa-943e-346ed45403ea + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A6DA + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15004 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.1 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_357_sample_0 + identifier: + - value: a2260bc1-8aa1-442c-933e-e4a05d46d802 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DA-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_357_sample_0_subject + identifier: + - value: TCGA-BA-A6DA-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 17885905-280f-40fa-943e-346ed45403ea + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 366 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_357_sample_1 + identifier: + - value: 33bf2824-d873-442f-8ae6-48274fbf4a94 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DA-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_357_sample_1_subject + identifier: + - value: TCGA-BA-A6DA-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 17885905-280f-40fa-943e-346ed45403ea + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_357_sample_2 + identifier: + - value: 8b80b922-b00f-4cda-92a2-49c357aea89d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DA-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_357_sample_2_subject + identifier: + - value: TCGA-BA-A6DA-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 17885905-280f-40fa-943e-346ed45403ea + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 366 + unit: + coding: *id001 + quantity_collected: + value_decimal: 250 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_358_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_358_diagnosis_0 + identifier: + - value: bfc1721c-c0de-54b3-9170-781b78cafd44 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_358 + identifier: + - value: ed61706c-7fc1-4c5f-b473-7b0888ac5b73 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-6868 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19608 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_358_sample_0 + identifier: + - value: ad04d034-7fff-4073-8c1f-97fac3d0bbdb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6868-01B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_358_sample_0_subject + identifier: + - value: TCGA-BA-6868-01B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ed61706c-7fc1-4c5f-b473-7b0888ac5b73 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_358_sample_1 + identifier: + - value: d660bc61-4016-4f52-98c3-72de5459946a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6868-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_358_sample_1_subject + identifier: + - value: TCGA-BA-6868-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ed61706c-7fc1-4c5f-b473-7b0888ac5b73 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_358_sample_2 + identifier: + - value: 0469c4d4-58ff-411d-9bf4-8d8bbe31d7c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-6868-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_358_sample_2_subject + identifier: + - value: TCGA-BA-6868-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ed61706c-7fc1-4c5f-b473-7b0888ac5b73 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_359_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_359_diagnosis_0 + identifier: + - value: d234a346-038c-58a0-824d-22bfabb73218 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_359 + identifier: + - value: 6ea380ad-d73d-41b2-b448-2d224deec01b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-MT-A51W + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19098 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C02.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_359_sample_0 + identifier: + - value: 03c6ac2c-c6b6-4041-a024-f2556fab62b8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MT-A51W-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_359_sample_0_subject + identifier: + - value: TCGA-MT-A51W-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ea380ad-d73d-41b2-b448-2d224deec01b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 49 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_359_sample_1 + identifier: + - value: d238e52b-b2e8-479e-b76c-a168136e0ef0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MT-A51W-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_359_sample_1_subject + identifier: + - value: TCGA-MT-A51W-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ea380ad-d73d-41b2-b448-2d224deec01b + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_359_sample_2 + identifier: + - value: 91e56a17-b4e8-4ef7-b587-a83bcd8c062d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MT-A51W-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_359_sample_2_subject + identifier: + - value: TCGA-MT-A51W-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6ea380ad-d73d-41b2-b448-2d224deec01b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 49 + unit: + coding: *id001 + quantity_collected: + value_decimal: 130 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_360_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_360_diagnosis_0 + identifier: + - value: f0a3480b-d52a-5db1-b03f-693a9bad5cfc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_360 + identifier: + - value: 17b17d91-c3df-4b89-9c10-4db069aff656 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-5559 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26286 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_360_sample_0 + identifier: + - value: 43fbb037-8ba4-4ba3-8458-71a027eda822 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5559-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_360_sample_0_subject + identifier: + - value: TCGA-BA-5559-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 17b17d91-c3df-4b89-9c10-4db069aff656 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_360_sample_1 + identifier: + - value: fbea64f9-b46b-4af1-bfb2-1791d93977b6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5559-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_360_sample_1_subject + identifier: + - value: TCGA-BA-5559-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 17b17d91-c3df-4b89-9c10-4db069aff656 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_360_sample_2 + identifier: + - value: 8c925c97-a7e0-44b3-ac62-b365e89975f0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5559-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_360_sample_2_subject + identifier: + - value: TCGA-BA-5559-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 17b17d91-c3df-4b89-9c10-4db069aff656 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_361_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_361_diagnosis_0 + identifier: + - value: 54c68cb3-653c-5035-829e-11c7b3853119 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_361 + identifier: + - value: 490950f3-2d1a-4174-a30d-b8f5654ff316 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7089 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27149 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2001-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_361_sample_0 + identifier: + - value: f2e436bd-bbc1-4b1d-9a55-e2a83a1bb510 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7089-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_361_sample_0_subject + identifier: + - value: TCGA-CV-7089-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 490950f3-2d1a-4174-a30d-b8f5654ff316 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_361_sample_1 + identifier: + - value: 7f11de1e-f75d-4476-a179-b50a84a45a78 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7089-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_361_sample_1_subject + identifier: + - value: TCGA-CV-7089-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 490950f3-2d1a-4174-a30d-b8f5654ff316 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_361_sample_2 + identifier: + - value: a6c24a00-67fd-4a1c-a371-b6e387dcea61 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7089-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_361_sample_2_subject + identifier: + - value: TCGA-CV-7089-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 490950f3-2d1a-4174-a30d-b8f5654ff316 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_361_sample_3 + identifier: + - value: 267e43c1-bf99-430a-b077-147985fb7e64 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7089-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_361_sample_3_subject + identifier: + - value: TCGA-CV-7089-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 490950f3-2d1a-4174-a30d-b8f5654ff316 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_362_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_362_diagnosis_0 + identifier: + - value: 740bf7b0-dfdd-4930-9cc7-3790cb8808c1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_362 + identifier: + - value: 9a8d612d-7809-41a5-adb7-736f0c98c903 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0005212 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_362_sample_0 + identifier: + - value: 6e2561a0-676c-4f69-9059-d49696a56c64 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0005212-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_362_sample_0_subject + identifier: + - value: GENIE-MSK-P-0005212-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9a8d612d-7809-41a5-adb7-736f0c98c903 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_363_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_363_diagnosis_0 + identifier: + - value: 7bfa067f-69be-4a58-a8a7-98963ee8c589 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_363 + identifier: + - value: 38f87d5c-b8d6-4447-90ff-c70bead7dcd7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-493620 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_363_sample_0 + identifier: + - value: 57a1d12e-9ead-43ed-8990-0fecb573d3cf + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-493620-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_363_sample_0_subject + identifier: + - value: GENIE-VICC-493620-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 38f87d5c-b8d6-4447-90ff-c70bead7dcd7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_364_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_364_diagnosis_0 + identifier: + - value: 28fc2416-e276-4a4c-963f-1ff59d64fb44 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_364 + identifier: + - value: 96f6abf6-569f-4eae-82e7-b5a784d6ca0a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-a947c792 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_364_sample_0 + identifier: + - value: cb69d223-6e16-4e94-8a35-b1197a261b19 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-a947c792-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_364_sample_0_subject + identifier: + - value: GENIE-GRCC-a947c792-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 96f6abf6-569f-4eae-82e7-b5a784d6ca0a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_365_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_365_diagnosis_0 + identifier: + - value: a099ae58-fa38-4a90-82b6-c97a23b317f0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_365 + identifier: + - value: be2774f4-7828-4216-b121-41e6115017a2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-f88a03a6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_365_sample_0 + identifier: + - value: a9b18808-3ee9-4274-9a83-8d2fcbc16c7f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-f88a03a6-metastasis-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_365_sample_0_subject + identifier: + - value: GENIE-GRCC-f88a03a6-metastasis-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: be2774f4-7828-4216-b121-41e6115017a2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_366_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_366_diagnosis_0 + identifier: + - value: 491f9f68-fb39-4d17-a75d-90d14e801df2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_366 + identifier: + - value: 7680b753-9c38-4454-91a7-677185632dbd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD15095 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15839 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_366_sample_0 + identifier: + - value: ae6cd26b-98b2-46a9-917b-cecd94358907 + system: http://crdc.nci.nih.gov/gdc + - value: AD15095_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_366_sample_0_subject + identifier: + - value: AD15095_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7680b753-9c38-4454-91a7-677185632dbd + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_367_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_367_diagnosis_0 + identifier: + - value: e7fe03ad-184c-46be-adcb-dcfc79db3492 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_367 + identifier: + - value: 13953e2c-65e9-4125-a0c1-3918dbe70ed8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-d47c6375 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_367_sample_0 + identifier: + - value: 7512ff60-162b-41b7-a3ed-c153d7aee073 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-d47c6375-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_367_sample_0_subject + identifier: + - value: GENIE-GRCC-d47c6375-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 13953e2c-65e9-4125-a0c1-3918dbe70ed8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_368_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_368_diagnosis_0 + identifier: + - value: c1887ffe-1e7a-4584-a9cb-897604949138 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_368 + identifier: + - value: 62cbb14f-5a1e-4113-97c6-2c304cc923f7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD7475 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18688 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_368_sample_0 + identifier: + - value: b82784b8-217d-487f-b2f6-4435ebc09885 + system: http://crdc.nci.nih.gov/gdc + - value: AD7475_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_368_sample_0_subject + identifier: + - value: AD7475_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 62cbb14f-5a1e-4113-97c6-2c304cc923f7 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_369_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_369_diagnosis_0 + identifier: + - value: d078cccf-6335-4c55-8d5e-a36e32dd8006 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_369 + identifier: + - value: 5538b049-618b-495b-92e8-6af23ae5351f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004034 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_369_sample_0 + identifier: + - value: 7d1a8a2e-c9d3-4e1d-b183-3c82de7e2306 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004034-372 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_369_sample_0_subject + identifier: + - value: GENIE-DFCI-004034-372 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5538b049-618b-495b-92e8-6af23ae5351f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_370_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_370_diagnosis_0 + identifier: + - value: 09912a9d-8fe7-4170-89cb-f0881ba681bb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_370 + identifier: + - value: 5d02b1bd-5f94-4b5a-9f47-6b2479027183 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037012 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_370_sample_0 + identifier: + - value: 89c7b64b-262a-440c-b2b0-b45a94097d6b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037012-88553 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_370_sample_0_subject + identifier: + - value: GENIE-DFCI-037012-88553 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d02b1bd-5f94-4b5a-9f47-6b2479027183 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_371_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_371_diagnosis_0 + identifier: + - value: 73adb3fc-a3c9-487c-a0d0-fa8b09707932 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_371 + identifier: + - value: 5d89add9-940b-4269-a75c-2b4ad6b695e4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005121 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_371_sample_0 + identifier: + - value: eadf6e9a-c6c3-444c-8e93-8ab77ed87d09 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005121-1375 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_371_sample_0_subject + identifier: + - value: GENIE-DFCI-005121-1375 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5d89add9-940b-4269-a75c-2b4ad6b695e4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_372_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_372_diagnosis_0 + identifier: + - value: 22080645-9bd1-4303-ae61-8228c254dc24 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_372 + identifier: + - value: 94e63b69-0096-4b52-93b1-e303e6910d62 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002746 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_372_sample_0 + identifier: + - value: c74deddd-6181-4108-baf3-4d750d877606 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002746-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_372_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002746-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 94e63b69-0096-4b52-93b1-e303e6910d62 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_373_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_373_diagnosis_0 + identifier: + - value: d813126a-5e28-5c5a-8730-598f0d047584 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_373 + identifier: + - value: 30ba94a6-bd7a-5d42-add6-c007b37888db + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TARGET-52-PATBLF + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 761 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Malignant rhabdoid tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8963/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_373_sample_0 + identifier: + - value: ac3e795d-69a1-57f5-9dec-5b59e2523091 + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PATBLF-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_373_sample_0_subject + identifier: + - value: TARGET-52-PATBLF-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 30ba94a6-bd7a-5d42-add6-c007b37888db + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_373_sample_1 + identifier: + - value: eb5eeeae-6bd7-511e-9f13-51531684c774 + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PATBLF-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_373_sample_1_subject + identifier: + - value: TARGET-52-PATBLF-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 30ba94a6-bd7a-5d42-add6-c007b37888db + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_374_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_374_diagnosis_0 + identifier: + - value: 9a11a042-337d-5a91-b483-093f98b0b72f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_374 + identifier: + - value: 26b56e63-cd15-52ee-aaf4-ca89354317d0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TARGET-52-PARKKN + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 2355 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Malignant rhabdoid tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8963/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_374_sample_0 + identifier: + - value: ced7edc7-a9ff-5d30-a63d-dbed4edfe497 + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PARKKN-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_374_sample_0_subject + identifier: + - value: TARGET-52-PARKKN-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 26b56e63-cd15-52ee-aaf4-ca89354317d0 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_375_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_375_diagnosis_0 + identifier: + - value: d1368e23-4a00-5b0c-ad28-56a5a4dbd833 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_375 + identifier: + - value: d3b488d6-aeee-5302-b291-b563a60416f5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TARGET-52-PATYUA + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 818 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Malignant rhabdoid tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8963/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_375_sample_0 + identifier: + - value: 83a37c0f-ac29-558c-b7dc-a9fcfed82b61 + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PATYUA-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_375_sample_0_subject + identifier: + - value: TARGET-52-PATYUA-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d3b488d6-aeee-5302-b291-b563a60416f5 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_376_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_376_diagnosis_0 + identifier: + - value: 2e79ab38-e511-5e60-8c81-1584d28a909e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_376 + identifier: + - value: 153c5c30-41d5-5369-873f-d086ead699a4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TARGET-52-PASVDP + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 141 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Malignant rhabdoid tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8963/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_376_sample_0 + identifier: + - value: fd9ff1de-6856-5a42-ad32-2e3aa28dc2d7 + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PASVDP-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_376_sample_0_subject + identifier: + - value: TARGET-52-PASVDP-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 153c5c30-41d5-5369-873f-d086ead699a4 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_376_sample_1 + identifier: + - value: a28e1682-4703-527b-bd4e-81f86fa6f35a + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PASVDP-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_376_sample_1_subject + identifier: + - value: TARGET-52-PASVDP-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 153c5c30-41d5-5369-873f-d086ead699a4 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_377_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_377_diagnosis_0 + identifier: + - value: cbc897af-ab20-50cf-b397-5bdaeadb4691 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_377 + identifier: + - value: ead9a4f1-e7d2-5341-93a0-a67267c28728 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TARGET-52-PASAMZ + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 3027 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Malignant rhabdoid tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8963/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_377_sample_0 + identifier: + - value: e5a4af40-c272-5aeb-942c-4be4614b4cfd + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PASAMZ-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_377_sample_0_subject + identifier: + - value: TARGET-52-PASAMZ-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ead9a4f1-e7d2-5341-93a0-a67267c28728 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_378_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_378_diagnosis_0 + identifier: + - value: 33c5c040-da3f-5e5f-8d13-ab9eff88f833 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_378 + identifier: + - value: 3649a820-6218-5187-8530-45a83b4a0b1a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TARGET-52-PASCDH + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 354 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Malignant rhabdoid tumor + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8963/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_378_sample_0 + identifier: + - value: 1d3eef26-a725-51f7-95fa-139d1a7da76e + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PASCDH-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_378_sample_0_subject + identifier: + - value: TARGET-52-PASCDH-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3649a820-6218-5187-8530-45a83b4a0b1a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_378_sample_1 + identifier: + - value: da724216-c1fe-5420-9e73-3a9d4b52bf1c + system: http://crdc.nci.nih.gov/gdc + - value: TARGET-52-PASCDH-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_378_sample_1_subject + identifier: + - value: TARGET-52-PASCDH-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3649a820-6218-5187-8530-45a83b4a0b1a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - method_type: + coding: + - code: None + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + specific_tissue_pathology: + coding: + - code: Rhabdoid tumor (kidney) (RT) + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_379_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_379_diagnosis_0 + identifier: + - value: dc412cff-36a3-4721-b1f3-8e16ed74489d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_379 + identifier: + - value: 9a7890c7-32d3-4586-a920-d6ed929622ce + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001186 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_379_sample_0 + identifier: + - value: 1853a05a-8846-4da3-9509-bff587eb6e8d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001186-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_379_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001186-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9a7890c7-32d3-4586-a920-d6ed929622ce + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_380_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_380_diagnosis_0 + identifier: + - value: b62e9fa2-da66-5eb2-b390-96985bc92b6b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_380 + identifier: + - value: b6d1490a-ae85-4e99-a053-1614b498a081 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-H7-A6C5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23808 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_380_sample_0 + identifier: + - value: 069b94fd-00fe-4073-bfca-3a3a8057d1f8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A6C5-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_380_sample_0_subject + identifier: + - value: TCGA-H7-A6C5-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b6d1490a-ae85-4e99-a053-1614b498a081 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_380_sample_1 + identifier: + - value: 578cf44a-2d2c-416d-a428-69547378bb9b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A6C5-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_380_sample_1_subject + identifier: + - value: TCGA-H7-A6C5-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b6d1490a-ae85-4e99-a053-1614b498a081 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 230 + unit: + coding: *id001 + quantity_collected: + value_decimal: 100 + unit: + coding: &id002 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_380_sample_2 + identifier: + - value: 875069b7-9411-4fb1-b8a2-992a052bee49 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A6C5-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_380_sample_2_subject + identifier: + - value: TCGA-H7-A6C5-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b6d1490a-ae85-4e99-a053-1614b498a081 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 230 + unit: + coding: *id001 + quantity_collected: + value_decimal: 150 + unit: + coding: *id002 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_380_sample_3 + identifier: + - value: 9b557922-d796-48bd-b194-1fba8622f254 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A6C5-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_380_sample_3_subject + identifier: + - value: TCGA-H7-A6C5-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b6d1490a-ae85-4e99-a053-1614b498a081 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 230 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_381_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_381_diagnosis_0 + identifier: + - value: c2494ea4-5db2-5716-9afd-096e152b592c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_381 + identifier: + - value: e1fed7aa-2bce-45ae-b0c6-7f50ef97e425 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5356 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20540 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_381_sample_0 + identifier: + - value: cf684788-d8e6-49da-8421-b2dbf040a529 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5356-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_381_sample_0_subject + identifier: + - value: TCGA-CN-5356-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e1fed7aa-2bce-45ae-b0c6-7f50ef97e425 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_381_sample_1 + identifier: + - value: fb9d2ba0-7673-4587-ab69-0059fce2f671 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5356-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_381_sample_1_subject + identifier: + - value: TCGA-CN-5356-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e1fed7aa-2bce-45ae-b0c6-7f50ef97e425 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_381_sample_2 + identifier: + - value: bcb5da85-78d6-4519-9740-378587b1bd37 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5356-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_381_sample_2_subject + identifier: + - value: TCGA-CN-5356-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e1fed7aa-2bce-45ae-b0c6-7f50ef97e425 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_382_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_382_diagnosis_0 + identifier: + - value: fd3fbe29-2fa3-41f7-99c9-51d3d05ff5b4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_382 + identifier: + - value: 7922c8b6-6de7-4810-93cc-5b4bf0654675 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003147 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_382_sample_0 + identifier: + - value: 13654c9a-afcc-4635-9885-8418a318ac7a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003147-99 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_382_sample_0_subject + identifier: + - value: GENIE-DFCI-003147-99 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7922c8b6-6de7-4810-93cc-5b4bf0654675 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_383_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_383_diagnosis_0 + identifier: + - value: 0b9b2b22-2fe6-5569-99ea-4647a15e68a0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_383 + identifier: + - value: c539274c-e2bf-4b5f-ab56-35eff1569bac + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7177 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 30180 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_383_sample_0 + identifier: + - value: ddb758e6-20a8-4a28-ba98-798de978154f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7177-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_383_sample_0_subject + identifier: + - value: TCGA-CV-7177-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c539274c-e2bf-4b5f-ab56-35eff1569bac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_383_sample_1 + identifier: + - value: e850a80d-1b50-4ab6-ab36-1d1a5e697d7e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7177-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_383_sample_1_subject + identifier: + - value: TCGA-CV-7177-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c539274c-e2bf-4b5f-ab56-35eff1569bac + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_383_sample_2 + identifier: + - value: 21152590-1224-410e-aaf7-4088302c809f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7177-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_383_sample_2_subject + identifier: + - value: TCGA-CV-7177-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c539274c-e2bf-4b5f-ab56-35eff1569bac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_383_sample_3 + identifier: + - value: 768e2bab-347b-4d90-887f-bf5692a91eb0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7177-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_383_sample_3_subject + identifier: + - value: TCGA-CV-7177-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c539274c-e2bf-4b5f-ab56-35eff1569bac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_384_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_384_diagnosis_0 + identifier: + - value: 3f9675d2-ad2f-5a88-af81-e7e9b5744c1a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_384 + identifier: + - value: a4cb2c52-15e2-45c8-aff9-23339217d167 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7437 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 28221 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1996-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_384_sample_0 + identifier: + - value: d7340d97-4ebd-4125-961a-9a5abe2f0ebb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7437-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_384_sample_0_subject + identifier: + - value: TCGA-CV-7437-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4cb2c52-15e2-45c8-aff9-23339217d167 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_384_sample_1 + identifier: + - value: 58c15c00-ddad-4f65-9f03-1882b7f9a09b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7437-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_384_sample_1_subject + identifier: + - value: TCGA-CV-7437-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4cb2c52-15e2-45c8-aff9-23339217d167 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_384_sample_2 + identifier: + - value: 215c17d6-2035-48da-9d06-c54734042898 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7437-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_384_sample_2_subject + identifier: + - value: TCGA-CV-7437-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4cb2c52-15e2-45c8-aff9-23339217d167 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_384_sample_3 + identifier: + - value: 46be59da-3e8e-43cb-a4f4-6658b12f1fe9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7437-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_384_sample_3_subject + identifier: + - value: TCGA-CV-7437-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4cb2c52-15e2-45c8-aff9-23339217d167 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_385_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_385_diagnosis_0 + identifier: + - value: da5ce97d-de12-5384-a88d-a9874b39b7dc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_385 + identifier: + - value: 2915b26b-8c18-48e4-9715-a7e207f0a0e6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A64Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 29037 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C04.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_385_sample_0 + identifier: + - value: eb25346e-0e28-4161-94c8-916b41f8d969 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A64Z-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_385_sample_0_subject + identifier: + - value: TCGA-QK-A64Z-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2915b26b-8c18-48e4-9715-a7e207f0a0e6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_385_sample_1 + identifier: + - value: 67289d96-8140-4ba1-9863-124950488c1d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A64Z-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_385_sample_1_subject + identifier: + - value: TCGA-QK-A64Z-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2915b26b-8c18-48e4-9715-a7e207f0a0e6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 555 + unit: + coding: *id001 + quantity_collected: + value_decimal: 80 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_385_sample_2 + identifier: + - value: 95525590-0eea-4017-be66-dc487b78299c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A64Z-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_385_sample_2_subject + identifier: + - value: TCGA-QK-A64Z-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2915b26b-8c18-48e4-9715-a7e207f0a0e6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 555 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_386_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_386_diagnosis_0 + identifier: + - value: 18a6869d-fcbd-526c-a71f-7f5145b12278 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_386 + identifier: + - value: 6715b957-0d48-439c-8cd7-bd9b204d39b0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7440 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 13992 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_386_sample_0 + identifier: + - value: 80eca6e9-b390-4878-a070-e40c1c19b1f4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7440-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_386_sample_0_subject + identifier: + - value: TCGA-CV-7440-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6715b957-0d48-439c-8cd7-bd9b204d39b0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_386_sample_1 + identifier: + - value: 1d594963-b5c3-496e-af52-5f6dbcd6910f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7440-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_386_sample_1_subject + identifier: + - value: TCGA-CV-7440-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6715b957-0d48-439c-8cd7-bd9b204d39b0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_386_sample_2 + identifier: + - value: 86b81c8d-ae15-477a-86fa-6e10f1263f87 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7440-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_386_sample_2_subject + identifier: + - value: TCGA-CV-7440-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6715b957-0d48-439c-8cd7-bd9b204d39b0 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_386_sample_3 + identifier: + - value: bb0c2fd4-8ffd-4825-aaf2-e865090940c8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7440-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_386_sample_3_subject + identifier: + - value: TCGA-CV-7440-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6715b957-0d48-439c-8cd7-bd9b204d39b0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_387_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_387_diagnosis_0 + identifier: + - value: 8d12f0ed-6345-50f9-aad6-68ae3ab8dbb1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_387 + identifier: + - value: 5436b002-4e4f-4d0f-9566-c0ef4d2d1854 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-RS-A6TP + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21393 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_387_sample_0 + identifier: + - value: 5d166131-946a-46de-b446-ea35d8b0e1a4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-RS-A6TP-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_387_sample_0_subject + identifier: + - value: TCGA-RS-A6TP-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5436b002-4e4f-4d0f-9566-c0ef4d2d1854 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_387_sample_1 + identifier: + - value: 281693cb-2d6f-4a42-af26-d807ea67a191 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-RS-A6TP-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_387_sample_1_subject + identifier: + - value: TCGA-RS-A6TP-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5436b002-4e4f-4d0f-9566-c0ef4d2d1854 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 117 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_387_sample_2 + identifier: + - value: 1ce08042-34c7-450e-b1f5-8cdf9bfc5a77 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-RS-A6TP-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_387_sample_2_subject + identifier: + - value: TCGA-RS-A6TP-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5436b002-4e4f-4d0f-9566-c0ef4d2d1854 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 117 + unit: + coding: *id001 + quantity_collected: + value_decimal: 400 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_388_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_388_diagnosis_0 + identifier: + - value: e87ea1cc-7728-4592-9eeb-04d09e11660b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_388 + identifier: + - value: 8f337700-7479-4a0f-b1ce-215e78363ede + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0005082 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_388_sample_0 + identifier: + - value: f9e5d21f-2ee2-41c2-b864-f43d6a8357aa + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0005082-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_388_sample_0_subject + identifier: + - value: GENIE-MSK-P-0005082-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8f337700-7479-4a0f-b1ce-215e78363ede + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_389_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_389_diagnosis_0 + identifier: + - value: 5d448af8-7478-4252-9043-772077929480 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_389 + identifier: + - value: db66c80c-3b80-41f8-8a9a-ff084e7e21bd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-023766 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_389_sample_0 + identifier: + - value: a3ca3ea8-6ea0-4585-8a50-294ca4c87a24 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-023766-23966 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_389_sample_0_subject + identifier: + - value: GENIE-DFCI-023766-23966 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: db66c80c-3b80-41f8-8a9a-ff084e7e21bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_390_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_390_diagnosis_0 + identifier: + - value: 1dc5e826-3f32-4d4d-8e2c-00fdbd76b393 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_390 + identifier: + - value: 3f4b9c2a-1385-4643-a4e8-37265d010184 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010503 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_390_sample_0 + identifier: + - value: 78c3f61a-5719-4604-8ebe-c21057d3e416 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010503-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_390_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010503-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3f4b9c2a-1385-4643-a4e8-37265d010184 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_391_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_391_diagnosis_0 + identifier: + - value: 4f08ca0e-bd9c-425c-9137-a8bc3654ff09 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_391 + identifier: + - value: 370dfa65-6a4c-4c23-a133-8edc03689862 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0004619 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_391_sample_0 + identifier: + - value: 407047a0-1065-4e67-aee6-a3a66998deb8 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0004619-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_391_sample_0_subject + identifier: + - value: GENIE-MSK-P-0004619-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 370dfa65-6a4c-4c23-a133-8edc03689862 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_392_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_392_diagnosis_0 + identifier: + - value: 1fdbf271-8b0c-5d7b-bacf-d883e0d0d054 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_392 + identifier: + - value: 5793879b-f663-4a10-9bd9-1acd2e189650 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5360 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25034 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_392_sample_0 + identifier: + - value: 740cef36-1319-4096-8ba3-8e6fce6282da + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5360-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_392_sample_0_subject + identifier: + - value: TCGA-CN-5360-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5793879b-f663-4a10-9bd9-1acd2e189650 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_392_sample_1 + identifier: + - value: 0c00768e-8b13-4b8e-80fc-b344740845f1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5360-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_392_sample_1_subject + identifier: + - value: TCGA-CN-5360-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5793879b-f663-4a10-9bd9-1acd2e189650 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_392_sample_2 + identifier: + - value: 9439bc03-9d26-454a-ba80-a0f5a4585656 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5360-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_392_sample_2_subject + identifier: + - value: TCGA-CN-5360-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5793879b-f663-4a10-9bd9-1acd2e189650 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_393_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_393_diagnosis_0 + identifier: + - value: f7044868-4f81-56df-87a1-58bd49f9c8cd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_393 + identifier: + - value: 67560840-70fb-45fd-8572-648f74811aec + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A6V7 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 14895 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_393_sample_0 + identifier: + - value: 69fe86c3-1e82-4583-9051-ffdb84224239 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A6V7-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_393_sample_0_subject + identifier: + - value: TCGA-CN-A6V7-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 67560840-70fb-45fd-8572-648f74811aec + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 118 + unit: + coding: *id001 + quantity_collected: + value_decimal: 160 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_393_sample_1 + identifier: + - value: ed5933bf-adaf-4bee-81fb-b1ec5782c248 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A6V7-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_393_sample_1_subject + identifier: + - value: TCGA-CN-A6V7-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 67560840-70fb-45fd-8572-648f74811aec + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 118 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_394_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_394_diagnosis_0 + identifier: + - value: 9e74f3f5-ab22-55d9-a79e-9884f3b0f109 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_394 + identifier: + - value: d7641ca1-a062-4dd2-9414-447af7311a84 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5374 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20464 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2007-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_394_sample_0 + identifier: + - value: 617df1e0-b075-4610-b6d5-8850786fea70 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5374-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_394_sample_0_subject + identifier: + - value: TCGA-CN-5374-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d7641ca1-a062-4dd2-9414-447af7311a84 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_394_sample_1 + identifier: + - value: 27fb0ae5-d8a1-46ac-ad3e-2464c52d9cfd + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5374-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_394_sample_1_subject + identifier: + - value: TCGA-CN-5374-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d7641ca1-a062-4dd2-9414-447af7311a84 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_394_sample_2 + identifier: + - value: 88000b86-9334-41ef-847d-6668d17ec62b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5374-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_394_sample_2_subject + identifier: + - value: TCGA-CN-5374-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d7641ca1-a062-4dd2-9414-447af7311a84 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_395_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_395_diagnosis_0 + identifier: + - value: 2b3b0e72-0926-5ed2-89c8-ffa1585d111f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_395 + identifier: + - value: 3fb3d96e-85ef-4071-a220-2382f8d9de82 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A6K1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23848 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_395_sample_0 + identifier: + - value: 09b49e67-34d8-496e-b42a-5123fb516cc0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A6K1-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_395_sample_0_subject + identifier: + - value: TCGA-CV-A6K1-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3fb3d96e-85ef-4071-a220-2382f8d9de82 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 549 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_395_sample_1 + identifier: + - value: 8ae503f5-a283-4bdf-8c82-de63f534bc85 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A6K1-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_395_sample_1_subject + identifier: + - value: TCGA-CV-A6K1-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3fb3d96e-85ef-4071-a220-2382f8d9de82 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_395_sample_2 + identifier: + - value: 43115789-cca5-4dc0-8377-e47b90c3f16f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A6K1-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_395_sample_2_subject + identifier: + - value: TCGA-CV-A6K1-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3fb3d96e-85ef-4071-a220-2382f8d9de82 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 549 + unit: + coding: *id001 + quantity_collected: + value_decimal: 20 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_396_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_396_diagnosis_0 + identifier: + - value: b07c0682-d50b-5680-97fc-8e709e21c064 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_396 + identifier: + - value: 5ed786f3-1d15-4079-bb8f-2f34ef305644 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-8568 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22796 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_396_sample_0 + identifier: + - value: c812093b-04ce-4d3f-841d-9b81de63fc38 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-8568-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_396_sample_0_subject + identifier: + - value: TCGA-D6-8568-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ed786f3-1d15-4079-bb8f-2f34ef305644 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_396_sample_1 + identifier: + - value: eac181d7-f8b8-4350-92aa-62d3fd1bd86b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-8568-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_396_sample_1_subject + identifier: + - value: TCGA-D6-8568-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ed786f3-1d15-4079-bb8f-2f34ef305644 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_396_sample_2 + identifier: + - value: 6f150e98-8b4e-44ee-953b-1692d76c8868 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-8568-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_396_sample_2_subject + identifier: + - value: TCGA-D6-8568-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ed786f3-1d15-4079-bb8f-2f34ef305644 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_397_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_397_diagnosis_0 + identifier: + - value: 1d13cc0a-da04-5925-8930-693f09cd6432 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_397 + identifier: + - value: ff38628e-8abe-44d6-8d3b-7cfe46bd2e35 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-T2-A6X0 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18114 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_397_sample_0 + identifier: + - value: 0416608e-19db-43b8-ac11-87406b0164d0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T2-A6X0-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_397_sample_0_subject + identifier: + - value: TCGA-T2-A6X0-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ff38628e-8abe-44d6-8d3b-7cfe46bd2e35 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 314 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_397_sample_1 + identifier: + - value: a4b8631d-80aa-4665-86b4-0caa7241da66 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T2-A6X0-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_397_sample_1_subject + identifier: + - value: TCGA-T2-A6X0-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ff38628e-8abe-44d6-8d3b-7cfe46bd2e35 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 314 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_397_sample_2 + identifier: + - value: 6f085b6d-6abf-4d89-a17a-89e6c7f8fcc2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T2-A6X0-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_397_sample_2_subject + identifier: + - value: TCGA-T2-A6X0-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ff38628e-8abe-44d6-8d3b-7cfe46bd2e35 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_398_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_398_diagnosis_0 + identifier: + - value: 39fa27e5-b36f-50e5-b173-1bb73a1ba5ba + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_398 + identifier: + - value: 31243867-8e9f-46e9-a213-b83544eb8028 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-6826 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23722 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_398_sample_0 + identifier: + - value: a31ecf7e-1838-412b-ac34-6fd8810739c9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6826-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_398_sample_0_subject + identifier: + - value: TCGA-D6-6826-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 31243867-8e9f-46e9-a213-b83544eb8028 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_398_sample_1 + identifier: + - value: 1737989d-8463-4761-b111-53e4fd396375 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6826-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_398_sample_1_subject + identifier: + - value: TCGA-D6-6826-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 31243867-8e9f-46e9-a213-b83544eb8028 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_398_sample_2 + identifier: + - value: 7aa13049-917a-4d7a-bceb-3c718ec8fb7a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6826-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_398_sample_2_subject + identifier: + - value: TCGA-D6-6826-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 31243867-8e9f-46e9-a213-b83544eb8028 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_399_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_399_diagnosis_0 + identifier: + - value: 21b7042c-de33-572f-a77e-98db817efd44 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_399 + identifier: + - value: a98263a5-cc90-4734-b6f1-f0108bfd5cac + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6492 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 28600 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C05.0 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_399_sample_0 + identifier: + - value: 9d258494-fb84-4435-aa3a-f5778ac061c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6492-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_399_sample_0_subject + identifier: + - value: TCGA-CR-6492-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a98263a5-cc90-4734-b6f1-f0108bfd5cac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_399_sample_1 + identifier: + - value: 2da6f33b-4a9f-4cf6-ad8f-873be656a6f8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6492-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_399_sample_1_subject + identifier: + - value: TCGA-CR-6492-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a98263a5-cc90-4734-b6f1-f0108bfd5cac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_400_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_400_diagnosis_0 + identifier: + - value: b4c1dd26-92ca-5bf7-b861-bff7f68e8436 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_400 + identifier: + - value: 3a2fe6da-5f3c-4ad8-b735-23adffe3fd6b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A6SW + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18536 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2005-01-01' + condition: + coding: + - code: Basaloid squamous cell carcinoma + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8083/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_400_sample_0 + identifier: + - value: 50e494e8-d48a-44ec-91b3-5755b42f70ee + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6SW-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_400_sample_0_subject + identifier: + - value: TCGA-P3-A6SW-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3a2fe6da-5f3c-4ad8-b735-23adffe3fd6b + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_400_sample_1 + identifier: + - value: dc6d258a-dba3-4186-bf89-9efb70a32365 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6SW-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_400_sample_1_subject + identifier: + - value: TCGA-P3-A6SW-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3a2fe6da-5f3c-4ad8-b735-23adffe3fd6b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 3039 + unit: + coding: *id001 + quantity_collected: + value_decimal: 40 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_400_sample_2 + identifier: + - value: 0b1a1f48-c58d-447a-be06-1f4e0c1c39d2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6SW-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_400_sample_2_subject + identifier: + - value: TCGA-P3-A6SW-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3a2fe6da-5f3c-4ad8-b735-23adffe3fd6b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 3039 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_401_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_401_diagnosis_0 + identifier: + - value: f351c260-09d7-594c-8347-292ae6f65f1f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_401 + identifier: + - value: 6f02648b-0c48-46ea-874a-407f951f0409 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A49B + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26155 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_401_sample_0 + identifier: + - value: a49128ea-01e4-4587-845b-6b26bafa1c29 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A49B-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_401_sample_0_subject + identifier: + - value: TCGA-CN-A49B-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6f02648b-0c48-46ea-874a-407f951f0409 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 394 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_401_sample_1 + identifier: + - value: 16b91d52-3168-44d9-bbbd-9f6e8b2582b6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A49B-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_401_sample_1_subject + identifier: + - value: TCGA-CN-A49B-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 6f02648b-0c48-46ea-874a-407f951f0409 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 394 + unit: + coding: *id001 + quantity_collected: + value_decimal: 270 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_402_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_402_diagnosis_0 + identifier: + - value: c97d4793-3b4b-521d-a274-2d1dfeda79ae + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_402 + identifier: + - value: e189f082-c748-43d4-96ce-0c381e376531 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7398 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19468 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_402_sample_0 + identifier: + - value: 13348e4e-8b8e-44b5-83e6-a1159a53ea35 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7398-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_402_sample_0_subject + identifier: + - value: TCGA-CR-7398-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e189f082-c748-43d4-96ce-0c381e376531 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_402_sample_1 + identifier: + - value: 251e8544-2c3c-4b31-a2b4-29b57e6ee4fd + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7398-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_402_sample_1_subject + identifier: + - value: TCGA-CR-7398-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e189f082-c748-43d4-96ce-0c381e376531 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_403_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_403_diagnosis_0 + identifier: + - value: 3ddf3ff8-b8b0-5525-8425-dbe1c27753b6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_403 + identifier: + - value: b9aac2a5-5ca9-4f57-ba02-b53904256467 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-IQ-A61I + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23035 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_403_sample_0 + identifier: + - value: f238d98a-1b53-4aae-8bdf-f85f0b9a066c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-A61I-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_403_sample_0_subject + identifier: + - value: TCGA-IQ-A61I-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b9aac2a5-5ca9-4f57-ba02-b53904256467 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_403_sample_1 + identifier: + - value: 68604eed-fd8f-4003-b9bf-ad0e1ecdf3b3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-A61I-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_403_sample_1_subject + identifier: + - value: TCGA-IQ-A61I-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b9aac2a5-5ca9-4f57-ba02-b53904256467 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 352 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_403_sample_2 + identifier: + - value: 19c823d3-c15b-4a1c-9a27-6ce489f3b640 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-A61I-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_403_sample_2_subject + identifier: + - value: TCGA-IQ-A61I-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b9aac2a5-5ca9-4f57-ba02-b53904256467 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 352 + unit: + coding: *id001 + quantity_collected: + value_decimal: 100 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_404_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_404_diagnosis_0 + identifier: + - value: c1cb359f-50c5-527d-941f-328d1d34f062 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_404 + identifier: + - value: ebd1be2c-35ca-45c0-9aba-9baf432114c1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-IQ-7630 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18131 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_404_sample_0 + identifier: + - value: 3b35e7e6-0e30-48be-9d22-d95fb49f1227 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-7630-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_404_sample_0_subject + identifier: + - value: TCGA-IQ-7630-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ebd1be2c-35ca-45c0-9aba-9baf432114c1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_404_sample_1 + identifier: + - value: d81234fd-4e10-469a-81e6-f23a192f1ef1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-7630-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_404_sample_1_subject + identifier: + - value: TCGA-IQ-7630-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ebd1be2c-35ca-45c0-9aba-9baf432114c1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_404_sample_2 + identifier: + - value: bd97a61f-6744-455f-88cf-2a418f2458a0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-7630-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_404_sample_2_subject + identifier: + - value: TCGA-IQ-7630-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ebd1be2c-35ca-45c0-9aba-9baf432114c1 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_405_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_405_diagnosis_0 + identifier: + - value: 388e26e6-e8e6-527b-929e-24ff75edc9b4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_405 + identifier: + - value: c72ae014-3c05-47f9-8615-6633467bc532 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5441 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21305 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2003-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_405_sample_0 + identifier: + - value: 26c67c48-00d3-4491-b761-7941415a2c6f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5441-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_405_sample_0_subject + identifier: + - value: TCGA-CV-5441-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c72ae014-3c05-47f9-8615-6633467bc532 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_405_sample_1 + identifier: + - value: b480eb37-ffe0-4626-b49d-dfc514a60886 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5441-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_405_sample_1_subject + identifier: + - value: TCGA-CV-5441-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c72ae014-3c05-47f9-8615-6633467bc532 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_405_sample_2 + identifier: + - value: 3f583e59-c92a-4257-8098-5d081642dea7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5441-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_405_sample_2_subject + identifier: + - value: TCGA-CV-5441-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c72ae014-3c05-47f9-8615-6633467bc532 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_406_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_406_diagnosis_0 + identifier: + - value: 7c2fbcc8-56e0-508a-84f8-97fb3ad6a8ab + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_406 + identifier: + - value: e7d49212-e9cb-4cd7-923a-bdfc82a4a150 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6011 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21016 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_406_sample_0 + identifier: + - value: 83b525ab-ad48-45fe-bbe9-54d6ce88054a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6011-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_406_sample_0_subject + identifier: + - value: TCGA-CN-6011-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e7d49212-e9cb-4cd7-923a-bdfc82a4a150 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_406_sample_1 + identifier: + - value: afbf3020-1715-4e74-8224-05e316796999 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6011-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_406_sample_1_subject + identifier: + - value: TCGA-CN-6011-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e7d49212-e9cb-4cd7-923a-bdfc82a4a150 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_406_sample_2 + identifier: + - value: 4d620a8e-517e-43b2-ad44-d9a8467e73a7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6011-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_406_sample_2_subject + identifier: + - value: TCGA-CN-6011-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e7d49212-e9cb-4cd7-923a-bdfc82a4a150 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_407_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_407_diagnosis_0 + identifier: + - value: cf93d012-b0b8-57b3-8a55-7575dfde2b1d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_407 + identifier: + - value: f33aa93f-b32d-4c4f-9a71-1e5ab69c6899 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6989 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23515 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_407_sample_0 + identifier: + - value: 3570ac4b-b585-4262-b54b-137a2515c689 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6989-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_407_sample_0_subject + identifier: + - value: TCGA-CN-6989-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f33aa93f-b32d-4c4f-9a71-1e5ab69c6899 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_407_sample_1 + identifier: + - value: 7ac8fb22-0a09-4b16-af8c-b5c2e90a968a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6989-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_407_sample_1_subject + identifier: + - value: TCGA-CN-6989-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f33aa93f-b32d-4c4f-9a71-1e5ab69c6899 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_407_sample_2 + identifier: + - value: a5c6b30f-2aa3-48bd-8415-bdce2444e49d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6989-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_407_sample_2_subject + identifier: + - value: TCGA-CN-6989-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f33aa93f-b32d-4c4f-9a71-1e5ab69c6899 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_408_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_408_diagnosis_0 + identifier: + - value: becd7cb0-9352-5c38-856c-fcfa539fdea3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_408 + identifier: + - value: 64bb5550-2735-4401-a0db-58ec1020a32d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5431 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26953 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_408_sample_0 + identifier: + - value: 39e3facf-6d13-4611-bcfa-90ef0350814d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5431-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_408_sample_0_subject + identifier: + - value: TCGA-CV-5431-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 64bb5550-2735-4401-a0db-58ec1020a32d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_408_sample_1 + identifier: + - value: be567c0a-3833-45d7-b846-d229a8e16e16 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5431-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_408_sample_1_subject + identifier: + - value: TCGA-CV-5431-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 64bb5550-2735-4401-a0db-58ec1020a32d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_408_sample_2 + identifier: + - value: 8897e2b3-1863-43c7-a84f-fe53d12371f9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5431-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_408_sample_2_subject + identifier: + - value: TCGA-CV-5431-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 64bb5550-2735-4401-a0db-58ec1020a32d + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_409_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_409_diagnosis_0 + identifier: + - value: 556216dd-a648-5f7e-a4b1-8f8688a354b6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_409 + identifier: + - value: 248fa778-0758-4681-a31f-371ea8d376e6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-4217 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25020 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_409_sample_0 + identifier: + - value: b9427fad-04aa-4e73-99ba-ccde04e4978b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4217-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_409_sample_0_subject + identifier: + - value: TCGA-BB-4217-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 248fa778-0758-4681-a31f-371ea8d376e6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_409_sample_1 + identifier: + - value: 5eacbcc3-8ac1-42bc-b3dd-53bc693d3cae + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4217-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_409_sample_1_subject + identifier: + - value: TCGA-BB-4217-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 248fa778-0758-4681-a31f-371ea8d376e6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_409_sample_2 + identifier: + - value: 3d9307b9-f42f-421b-bebe-ed692a5868ce + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4217-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_409_sample_2_subject + identifier: + - value: TCGA-BB-4217-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 248fa778-0758-4681-a31f-371ea8d376e6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_410_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_410_diagnosis_0 + identifier: + - value: f44a9ab8-f121-59c5-8087-567864266629 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_410 + identifier: + - value: 60fcc18c-0509-4c7b-aca9-178f47055077 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A63Y + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17125 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_410_sample_0 + identifier: + - value: e0b45d74-3b6e-424f-86e7-2174d7c1245a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63Y-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_410_sample_0_subject + identifier: + - value: TCGA-CN-A63Y-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 60fcc18c-0509-4c7b-aca9-178f47055077 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 167 + unit: + coding: *id001 + quantity_collected: + value_decimal: 200 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_410_sample_1 + identifier: + - value: daaeaef7-3f0f-4155-908d-9aa6e536f94c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63Y-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_410_sample_1_subject + identifier: + - value: TCGA-CN-A63Y-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 60fcc18c-0509-4c7b-aca9-178f47055077 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_410_sample_2 + identifier: + - value: 50cca7c4-4586-43cd-a59e-3fdc646f5aba + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A63Y-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_410_sample_2_subject + identifier: + - value: TCGA-CN-A63Y-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 60fcc18c-0509-4c7b-aca9-178f47055077 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 167 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_411_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_411_diagnosis_0 + identifier: + - value: 2602d676-8c2e-5bdd-9790-a0a072d3f670 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_411 + identifier: + - value: 0f25d7fd-fc7c-4563-a8bd-80b5e0c32ea2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-DQ-7596 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17846 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_411_sample_0 + identifier: + - value: f662e970-6a51-4164-8458-61e7ff054806 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7596-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_411_sample_0_subject + identifier: + - value: TCGA-DQ-7596-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0f25d7fd-fc7c-4563-a8bd-80b5e0c32ea2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_411_sample_1 + identifier: + - value: 61c82e56-e64e-4fcb-bc5f-dc4fe34b6c58 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7596-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_411_sample_1_subject + identifier: + - value: TCGA-DQ-7596-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0f25d7fd-fc7c-4563-a8bd-80b5e0c32ea2 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_411_sample_2 + identifier: + - value: 7a94106d-5604-4b73-9c54-54a72b12f52d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7596-10D + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_411_sample_2_subject + identifier: + - value: TCGA-DQ-7596-10D + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0f25d7fd-fc7c-4563-a8bd-80b5e0c32ea2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 560 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_412_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_412_diagnosis_0 + identifier: + - value: f41a7343-e52e-5f4b-b902-ccd3275b00b9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_412 + identifier: + - value: 4648225e-5b68-488a-969a-e8d812190c6f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-DQ-7589 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25606 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_412_sample_0 + identifier: + - value: 41ec6e82-6bcd-4057-a370-bfe1801e2e94 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7589-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_412_sample_0_subject + identifier: + - value: TCGA-DQ-7589-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4648225e-5b68-488a-969a-e8d812190c6f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_412_sample_1 + identifier: + - value: 19c44a45-4f80-4d5a-beac-83db256a3434 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7589-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_412_sample_1_subject + identifier: + - value: TCGA-DQ-7589-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4648225e-5b68-488a-969a-e8d812190c6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_412_sample_2 + identifier: + - value: e22036a1-ed2f-44b4-8bca-bd9808611fd0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-DQ-7589-10C + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_412_sample_2_subject + identifier: + - value: TCGA-DQ-7589-10C + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4648225e-5b68-488a-969a-e8d812190c6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_413_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_413_diagnosis_0 + identifier: + - value: 31489596-1797-567e-814f-ec85278ee342 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_413 + identifier: + - value: d89b1fd6-bef4-4803-8ed3-3b442be600b6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5432 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25006 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_413_sample_0 + identifier: + - value: 418aadda-9f2f-43be-b171-866585aab114 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5432-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_413_sample_0_subject + identifier: + - value: TCGA-CV-5432-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d89b1fd6-bef4-4803-8ed3-3b442be600b6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_413_sample_1 + identifier: + - value: b4a36114-80d3-4f28-b85a-077dc31eb485 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5432-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_413_sample_1_subject + identifier: + - value: TCGA-CV-5432-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d89b1fd6-bef4-4803-8ed3-3b442be600b6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_413_sample_2 + identifier: + - value: 3a13692e-cb77-464a-8ace-cba47f99247f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5432-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_413_sample_2_subject + identifier: + - value: TCGA-CV-5432-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d89b1fd6-bef4-4803-8ed3-3b442be600b6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_413_sample_3 + identifier: + - value: c552cf29-896d-4a47-8022-e5c57e27e70e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5432-11B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_413_sample_3_subject + identifier: + - value: TCGA-CV-5432-11B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d89b1fd6-bef4-4803-8ed3-3b442be600b6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_414_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_414_diagnosis_0 + identifier: + - value: 73fd5157-4aa2-5b2e-852b-889d058a6f8f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_414 + identifier: + - value: 30eb06a5-8e88-4c46-bebb-fb93ca07f108 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5366 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18904 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_414_sample_0 + identifier: + - value: f3e5a16f-7c16-425e-8321-b6b19fd469d3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5366-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_414_sample_0_subject + identifier: + - value: TCGA-CN-5366-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 30eb06a5-8e88-4c46-bebb-fb93ca07f108 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_414_sample_1 + identifier: + - value: 111ad944-f78e-4ec6-967b-f05c49b49b1c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5366-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_414_sample_1_subject + identifier: + - value: TCGA-CN-5366-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 30eb06a5-8e88-4c46-bebb-fb93ca07f108 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_414_sample_2 + identifier: + - value: 62fdf8f3-a028-453f-b27c-c2506be68cbe + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5366-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_414_sample_2_subject + identifier: + - value: TCGA-CN-5366-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 30eb06a5-8e88-4c46-bebb-fb93ca07f108 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_415_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_415_diagnosis_0 + identifier: + - value: e89ecbde-44e3-5db5-be20-af6cddaa4e92 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_415 + identifier: + - value: 731f6967-5a01-40b7-9f88-64d980214bb2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-T2-A6X2 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 30013 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_415_sample_0 + identifier: + - value: fe1541c0-a239-428f-bf43-8b8b999d362e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T2-A6X2-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_415_sample_0_subject + identifier: + - value: TCGA-T2-A6X2-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 731f6967-5a01-40b7-9f88-64d980214bb2 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_415_sample_1 + identifier: + - value: 0080b5ac-b9b2-4fef-ae51-6a6178325364 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T2-A6X2-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_415_sample_1_subject + identifier: + - value: TCGA-T2-A6X2-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 731f6967-5a01-40b7-9f88-64d980214bb2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 880 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_415_sample_2 + identifier: + - value: 161b6a0e-0b50-41a1-bdf3-bd7666067454 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T2-A6X2-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_415_sample_2_subject + identifier: + - value: TCGA-T2-A6X2-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 731f6967-5a01-40b7-9f88-64d980214bb2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 880 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_416_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_416_diagnosis_0 + identifier: + - value: 6ce57628-3cd7-5cfd-8317-cadf76a37f43 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_416 + identifier: + - value: d83b6b2d-932b-4240-b99d-5506f18af892 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-7870 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21443 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_416_sample_0 + identifier: + - value: f5589c89-0b94-4492-8a3c-84d58377e94f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7870-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_416_sample_0_subject + identifier: + - value: TCGA-BB-7870-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d83b6b2d-932b-4240-b99d-5506f18af892 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_416_sample_1 + identifier: + - value: b79164b1-7abb-4585-b23a-0e610734ea8b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7870-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_416_sample_1_subject + identifier: + - value: TCGA-BB-7870-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d83b6b2d-932b-4240-b99d-5506f18af892 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_416_sample_2 + identifier: + - value: 0d53784e-011f-4890-9cf5-59e955dd1fea + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7870-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_416_sample_2_subject + identifier: + - value: TCGA-BB-7870-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d83b6b2d-932b-4240-b99d-5506f18af892 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_417_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_417_diagnosis_0 + identifier: + - value: eac797ee-ffad-5c80-8f0a-7e95590e118d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_417 + identifier: + - value: 5422a86d-f9ff-4fb6-873e-bf7cc3de50e5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7389 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20169 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2007-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_417_sample_0 + identifier: + - value: 6e926ab9-e086-48cb-876d-d490c46cb7f0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7389-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_417_sample_0_subject + identifier: + - value: TCGA-CR-7389-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5422a86d-f9ff-4fb6-873e-bf7cc3de50e5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_417_sample_1 + identifier: + - value: 9c35c1ec-5ca6-4900-aa39-ab1c962b9c4d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7389-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_417_sample_1_subject + identifier: + - value: TCGA-CR-7389-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5422a86d-f9ff-4fb6-873e-bf7cc3de50e5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_418_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_418_diagnosis_0 + identifier: + - value: c0dca6b0-81eb-598e-9514-f23513df1ab8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_418 + identifier: + - value: 32aac152-322b-4d7f-a78b-448fecdf17bf + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A71D + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19747 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_418_sample_0 + identifier: + - value: 297ea792-1a29-44db-a14b-38513b50826f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A71D-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_418_sample_0_subject + identifier: + - value: TCGA-UF-A71D-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 32aac152-322b-4d7f-a78b-448fecdf17bf + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 950 + unit: + coding: *id001 + quantity_collected: + value_decimal: 120 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_418_sample_1 + identifier: + - value: e4157201-93f3-4f08-b3a9-dacb22671a57 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A71D-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_418_sample_1_subject + identifier: + - value: TCGA-UF-A71D-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 32aac152-322b-4d7f-a78b-448fecdf17bf + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1055 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_418_sample_2 + identifier: + - value: 87d8fec9-7ac3-4359-a6be-de270584ac1b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A71D-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_418_sample_2_subject + identifier: + - value: TCGA-UF-A71D-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 32aac152-322b-4d7f-a78b-448fecdf17bf + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_419_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_419_diagnosis_0 + identifier: + - value: 7ed3e77f-cc81-56cb-b573-cc6df309ff48 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_419 + identifier: + - value: b8ac8500-abcd-40c4-9c24-7af557fd260a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-4227 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24322 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_419_sample_0 + identifier: + - value: f31d010d-cb3e-46da-9647-38fdb9d1bbc0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4227-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_419_sample_0_subject + identifier: + - value: TCGA-BB-4227-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b8ac8500-abcd-40c4-9c24-7af557fd260a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_419_sample_1 + identifier: + - value: a6748675-5433-4f39-a578-9a1ddb8bb1b3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4227-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_419_sample_1_subject + identifier: + - value: TCGA-BB-4227-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b8ac8500-abcd-40c4-9c24-7af557fd260a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_419_sample_2 + identifier: + - value: 0e81b0ef-6f16-4a56-9f18-8acad8bf9ccf + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-4227-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_419_sample_2_subject + identifier: + - value: TCGA-BB-4227-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b8ac8500-abcd-40c4-9c24-7af557fd260a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_420_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_420_diagnosis_0 + identifier: + - value: 92f6368e-51fb-56bf-a72d-7ccc16eafb44 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_420 + identifier: + - value: dbe29e97-f111-41d3-a25f-3b9eb9bb099f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5434 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22182 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_420_sample_0 + identifier: + - value: dc649d39-482d-4855-b9e3-129552e5e421 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5434-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_420_sample_0_subject + identifier: + - value: TCGA-CV-5434-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbe29e97-f111-41d3-a25f-3b9eb9bb099f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_420_sample_1 + identifier: + - value: 657cf588-cca0-44c2-83b3-0e87f7a81f29 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5434-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_420_sample_1_subject + identifier: + - value: TCGA-CV-5434-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbe29e97-f111-41d3-a25f-3b9eb9bb099f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_420_sample_2 + identifier: + - value: f6130e55-1627-4d2f-bd8f-c0e778a1aa45 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5434-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_420_sample_2_subject + identifier: + - value: TCGA-CV-5434-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbe29e97-f111-41d3-a25f-3b9eb9bb099f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_420_sample_3 + identifier: + - value: 3f70e2db-b313-4f3f-89e7-cd1c0acecf9b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5434-11B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_420_sample_3_subject + identifier: + - value: TCGA-CV-5434-11B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbe29e97-f111-41d3-a25f-3b9eb9bb099f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_421_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_421_diagnosis_0 + identifier: + - value: a71bc3c7-5807-5766-8487-c3dbc27484cb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_421 + identifier: + - value: e37f479f-ca05-45e4-ac6d-a974bed6e7f8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-5243 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18812 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2003-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_421_sample_0 + identifier: + - value: d89d46ea-9a7a-4fd8-b11e-9c9ca4780119 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5243-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_421_sample_0_subject + identifier: + - value: TCGA-CR-5243-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e37f479f-ca05-45e4-ac6d-a974bed6e7f8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_421_sample_1 + identifier: + - value: 6fc08372-0d9d-4b3c-b656-9573fa532c99 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5243-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_421_sample_1_subject + identifier: + - value: TCGA-CR-5243-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e37f479f-ca05-45e4-ac6d-a974bed6e7f8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_422_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_422_diagnosis_0 + identifier: + - value: 22e091bf-8af8-5910-9664-c73e7b5f44fb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_422 + identifier: + - value: 9ae5101b-6031-4ab1-bfca-198c41af3184 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6487 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18331 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_422_sample_0 + identifier: + - value: 027dedd3-bd53-420e-b7f2-eb5b8c26bcdc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6487-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_422_sample_0_subject + identifier: + - value: TCGA-CR-6487-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9ae5101b-6031-4ab1-bfca-198c41af3184 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_422_sample_1 + identifier: + - value: ff63290d-0644-4387-99bb-697150a7fb6b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6487-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_422_sample_1_subject + identifier: + - value: TCGA-CR-6487-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9ae5101b-6031-4ab1-bfca-198c41af3184 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_423_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_423_diagnosis_0 + identifier: + - value: eb8958ba-0798-5ab3-b4f4-258d441d7e03 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_423 + identifier: + - value: 46625ebd-5bf3-4fe7-bf3f-19cc5a210555 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A6T5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 28977 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.1 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_423_sample_0 + identifier: + - value: e45c81dc-4143-4e97-8212-85032c760221 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6T5-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_423_sample_0_subject + identifier: + - value: TCGA-P3-A6T5-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 46625ebd-5bf3-4fe7-bf3f-19cc5a210555 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1364 + unit: + coding: *id001 + quantity_collected: + value_decimal: 40 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_423_sample_1 + identifier: + - value: c98f1b7e-5d3c-4e07-9d9c-65c5a6ac6cd6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6T5-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_423_sample_1_subject + identifier: + - value: TCGA-P3-A6T5-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 46625ebd-5bf3-4fe7-bf3f-19cc5a210555 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1364 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_423_sample_2 + identifier: + - value: 7fddfc05-49ef-4ebc-8572-05059a5fc363 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6T5-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_423_sample_2_subject + identifier: + - value: TCGA-P3-A6T5-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 46625ebd-5bf3-4fe7-bf3f-19cc5a210555 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_424_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_424_diagnosis_0 + identifier: + - value: d80aa9c7-2a22-57da-87ef-750dd4c0b494 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_424 + identifier: + - value: b835289f-6174-4bf9-aedf-9ebb9ef4eb62 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-IQ-A61O + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15920 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, spindle cell + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C01 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8074/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_424_sample_0 + identifier: + - value: 09e8433c-1f86-42c5-91c0-2512fc4a7fe9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-A61O-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_424_sample_0_subject + identifier: + - value: TCGA-IQ-A61O-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b835289f-6174-4bf9-aedf-9ebb9ef4eb62 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 288 + unit: + coding: *id001 + quantity_collected: + value_decimal: 130 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_424_sample_1 + identifier: + - value: eee85b30-6d16-4f53-aac1-b74f36a62d9a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-A61O-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_424_sample_1_subject + identifier: + - value: TCGA-IQ-A61O-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b835289f-6174-4bf9-aedf-9ebb9ef4eb62 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 288 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_424_sample_2 + identifier: + - value: 24e39735-725e-4627-82b6-c56ff33e3465 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-IQ-A61O-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_424_sample_2_subject + identifier: + - value: TCGA-IQ-A61O-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b835289f-6174-4bf9-aedf-9ebb9ef4eb62 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_425_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_425_diagnosis_0 + identifier: + - value: 1e1fa97c-cb95-5810-9f22-9af6a0a42ce2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_425 + identifier: + - value: ba9d4568-71a8-41fc-a2be-0bf784e36d6a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6480 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19472 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_425_sample_0 + identifier: + - value: 0c6b4631-381e-4b73-ac9e-62bbc1849ff4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6480-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_425_sample_0_subject + identifier: + - value: TCGA-CR-6480-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ba9d4568-71a8-41fc-a2be-0bf784e36d6a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_425_sample_1 + identifier: + - value: e49031dd-14f3-4f2c-8457-d0249c491ae9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6480-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_425_sample_1_subject + identifier: + - value: TCGA-CR-6480-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ba9d4568-71a8-41fc-a2be-0bf784e36d6a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_426_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_426_diagnosis_0 + identifier: + - value: b7c4b294-1897-5001-8494-cedac0a7f991 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_426 + identifier: + - value: 10d0a058-3e5e-4916-84c4-25f934b96f86 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5440 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19197 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2002-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_426_sample_0 + identifier: + - value: 3f9a9578-e8e6-47b7-af7b-31d9cffbfd3a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5440-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_426_sample_0_subject + identifier: + - value: TCGA-CV-5440-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10d0a058-3e5e-4916-84c4-25f934b96f86 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_426_sample_1 + identifier: + - value: 28780b51-0b53-4d73-b399-ec90b45de0d3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5440-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_426_sample_1_subject + identifier: + - value: TCGA-CV-5440-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10d0a058-3e5e-4916-84c4-25f934b96f86 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_426_sample_2 + identifier: + - value: d773747d-fd09-4890-a436-9b212e19063b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5440-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_426_sample_2_subject + identifier: + - value: TCGA-CV-5440-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10d0a058-3e5e-4916-84c4-25f934b96f86 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_427_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_427_diagnosis_0 + identifier: + - value: 87e9b232-8b59-573b-9758-c7b5456d6fc0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_427 + identifier: + - value: 34227de4-d23c-46d6-b78b-49add24a4b88 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7248 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23082 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2001-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_427_sample_0 + identifier: + - value: 24a2dd45-0453-4bfa-af4c-cde8cb0c0cfb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7248-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_427_sample_0_subject + identifier: + - value: TCGA-CV-7248-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 34227de4-d23c-46d6-b78b-49add24a4b88 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_427_sample_1 + identifier: + - value: 5fe254fc-76cd-4081-a46f-574f2ec76d10 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7248-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_427_sample_1_subject + identifier: + - value: TCGA-CV-7248-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 34227de4-d23c-46d6-b78b-49add24a4b88 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_427_sample_2 + identifier: + - value: e5ab53bf-073a-49e7-9402-8e7261d385c8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7248-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_427_sample_2_subject + identifier: + - value: TCGA-CV-7248-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 34227de4-d23c-46d6-b78b-49add24a4b88 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_427_sample_3 + identifier: + - value: 791203c3-4192-4844-b32a-0f21944333e1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7248-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_427_sample_3_subject + identifier: + - value: TCGA-CV-7248-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 34227de4-d23c-46d6-b78b-49add24a4b88 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_428_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_428_diagnosis_0 + identifier: + - value: ce208b92-611f-5ffc-8a6f-b01b91e7b58b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_428 + identifier: + - value: 9f771c36-16ec-4770-bc53-f6c861343f1c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-6474 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18840 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_428_sample_0 + identifier: + - value: d84c30b6-e217-4b2c-9dc1-16428264378d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6474-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_428_sample_0_subject + identifier: + - value: TCGA-CR-6474-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9f771c36-16ec-4770-bc53-f6c861343f1c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_428_sample_1 + identifier: + - value: ddad5854-74a2-4db5-94d1-41196a37be5e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-6474-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_428_sample_1_subject + identifier: + - value: TCGA-CR-6474-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9f771c36-16ec-4770-bc53-f6c861343f1c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_429_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_429_diagnosis_0 + identifier: + - value: f09803e3-8795-5077-84ae-bf0666bedc35 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_429 + identifier: + - value: cc23a09b-bca7-43e0-9ad0-bf272848492e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5435 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20926 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_429_sample_0 + identifier: + - value: 14098d2a-e40e-4f1a-bd76-f8bf7c339ee5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5435-11B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_429_sample_0_subject + identifier: + - value: TCGA-CV-5435-11B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cc23a09b-bca7-43e0-9ad0-bf272848492e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_429_sample_1 + identifier: + - value: d2491655-a4a1-4e4b-8f94-f50dc1c5d64c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5435-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_429_sample_1_subject + identifier: + - value: TCGA-CV-5435-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cc23a09b-bca7-43e0-9ad0-bf272848492e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_429_sample_2 + identifier: + - value: cbcd3026-9f65-45c1-8fd8-d08f1b6b065e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5435-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_429_sample_2_subject + identifier: + - value: TCGA-CV-5435-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cc23a09b-bca7-43e0-9ad0-bf272848492e + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_429_sample_3 + identifier: + - value: 78a9bb84-9d21-40d2-9b0b-1ba8d888912d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5435-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_429_sample_3_subject + identifier: + - value: TCGA-CV-5435-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cc23a09b-bca7-43e0-9ad0-bf272848492e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_430_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_430_diagnosis_0 + identifier: + - value: 589f8f36-79a2-513f-a83e-cd707818b834 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_430 + identifier: + - value: a0b136fb-3a0a-4411-8907-4ca775c7d04e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-HD-A634 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20810 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_430_sample_0 + identifier: + - value: 34c0ddaa-1fcf-4e5c-b5bf-7cfae596c09d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-A634-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_430_sample_0_subject + identifier: + - value: TCGA-HD-A634-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a0b136fb-3a0a-4411-8907-4ca775c7d04e + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_430_sample_1 + identifier: + - value: c25592d6-b3d3-47b6-a3c5-3cbc81803152 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-A634-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_430_sample_1_subject + identifier: + - value: TCGA-HD-A634-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a0b136fb-3a0a-4411-8907-4ca775c7d04e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 41 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_430_sample_2 + identifier: + - value: 1bae9a44-1ce3-45b1-9902-40faeba58120 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-A634-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_430_sample_2_subject + identifier: + - value: TCGA-HD-A634-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a0b136fb-3a0a-4411-8907-4ca775c7d04e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 41 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_431_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_431_diagnosis_0 + identifier: + - value: 2457e378-c4bb-516f-8966-82e1453eafd7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_431 + identifier: + - value: e08ff4f7-62fd-4240-9e8b-c3ad7a9b2c44 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A460 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26539 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2001-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 5th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_431_sample_0 + identifier: + - value: 904d5793-ae7f-492b-aaed-ea6cca865d63 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A460-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_431_sample_0_subject + identifier: + - value: TCGA-CV-A460-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e08ff4f7-62fd-4240-9e8b-c3ad7a9b2c44 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4002 + unit: + coding: *id001 + quantity_collected: + value_decimal: 220 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_431_sample_1 + identifier: + - value: b1c47b2e-ba48-4f1f-b07e-f930b1135201 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A460-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_431_sample_1_subject + identifier: + - value: TCGA-CV-A460-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e08ff4f7-62fd-4240-9e8b-c3ad7a9b2c44 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4002 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_431_sample_2 + identifier: + - value: 9e397756-8535-40f2-9fc8-d0f1392a5e6d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A460-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_431_sample_2_subject + identifier: + - value: TCGA-CV-A460-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e08ff4f7-62fd-4240-9e8b-c3ad7a9b2c44 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_432_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_432_diagnosis_0 + identifier: + - value: 126d74e6-2981-5aea-80e7-62ec5cff609a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_432 + identifier: + - value: 7e3b90c1-8772-4e12-8050-a156558beb82 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4739 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26081 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_432_sample_0 + identifier: + - value: f450dbe6-4972-4c49-af97-963bcd0d0da0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4739-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_432_sample_0_subject + identifier: + - value: TCGA-CN-4739-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7e3b90c1-8772-4e12-8050-a156558beb82 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_432_sample_1 + identifier: + - value: b916fa4a-1d15-4619-9d6c-1000e96b7e0d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4739-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_432_sample_1_subject + identifier: + - value: TCGA-CN-4739-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7e3b90c1-8772-4e12-8050-a156558beb82 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_432_sample_2 + identifier: + - value: 9491d6f0-1e3e-48e5-aabb-87704511904b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4739-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_432_sample_2_subject + identifier: + - value: TCGA-CN-4739-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7e3b90c1-8772-4e12-8050-a156558beb82 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_433_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_433_diagnosis_0 + identifier: + - value: bd9d72bf-8331-5bd7-a4bc-1522518d3fb7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_433 + identifier: + - value: 1c801a6b-8407-46da-b6cc-245f05418b9e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A468 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 15372 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2001-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C00.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 5th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_433_sample_0 + identifier: + - value: 54fda578-dfb1-4a1b-8b01-2b7e9292f387 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A468-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_433_sample_0_subject + identifier: + - value: TCGA-CV-A468-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1c801a6b-8407-46da-b6cc-245f05418b9e + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_433_sample_1 + identifier: + - value: 66643338-ed21-460e-a1dc-b547c5b14500 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A468-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_433_sample_1_subject + identifier: + - value: TCGA-CV-A468-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1c801a6b-8407-46da-b6cc-245f05418b9e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4183 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_433_sample_2 + identifier: + - value: 7dc1e99f-c601-48c2-8326-389d9f084e29 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A468-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_433_sample_2_subject + identifier: + - value: TCGA-CV-A468-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1c801a6b-8407-46da-b6cc-245f05418b9e + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4183 + unit: + coding: *id001 + quantity_collected: + value_decimal: 220 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_434_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_434_diagnosis_0 + identifier: + - value: 9461c5ae-cbec-5810-b0a6-9644168accb4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_434 + identifier: + - value: 96163e94-4a14-4907-a57a-cfab4caf19a4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4723 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24815 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_434_sample_0 + identifier: + - value: f4a14404-3545-44fc-953d-e441139e7fda + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4723-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_434_sample_0_subject + identifier: + - value: TCGA-CN-4723-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 96163e94-4a14-4907-a57a-cfab4caf19a4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_434_sample_1 + identifier: + - value: 4db1536b-23d0-48fb-91f8-248a03f58aa4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4723-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_434_sample_1_subject + identifier: + - value: TCGA-CN-4723-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 96163e94-4a14-4907-a57a-cfab4caf19a4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_434_sample_2 + identifier: + - value: 4a485f87-1a73-42ec-af0d-0b6de2b23504 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4723-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_434_sample_2_subject + identifier: + - value: TCGA-CN-4723-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 96163e94-4a14-4907-a57a-cfab4caf19a4 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_435_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_435_diagnosis_0 + identifier: + - value: 91287016-0fd4-5434-a010-e392bd679282 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_435 + identifier: + - value: 468061c2-0acb-4f67-a357-99ccbd81a8b7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A45Y + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22442 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 5th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_435_sample_0 + identifier: + - value: bbcc5141-d805-457d-bc4a-d424c8c39cb7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45Y-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_435_sample_0_subject + identifier: + - value: TCGA-CV-A45Y-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 468061c2-0acb-4f67-a357-99ccbd81a8b7 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4481 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_435_sample_1 + identifier: + - value: 01a4aa4a-f073-435c-a411-839760cbcb9f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45Y-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_435_sample_1_subject + identifier: + - value: TCGA-CV-A45Y-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 468061c2-0acb-4f67-a357-99ccbd81a8b7 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_435_sample_2 + identifier: + - value: 26026e2f-b112-4535-97ac-6956cb267e9e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45Y-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_435_sample_2_subject + identifier: + - value: TCGA-CV-A45Y-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 468061c2-0acb-4f67-a357-99ccbd81a8b7 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 4481 + unit: + coding: *id001 + quantity_collected: + value_decimal: 30 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_436_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_436_diagnosis_0 + identifier: + - value: f7be786a-80e5-5c78-af12-715c8cdd318f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_436 + identifier: + - value: 2135b007-b714-495b-9b30-92010179ec33 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A718 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22836 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_436_sample_0 + identifier: + - value: a88696d9-b36a-4fd7-b3ed-b6b31aa4094f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A718-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_436_sample_0_subject + identifier: + - value: TCGA-UF-A718-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2135b007-b714-495b-9b30-92010179ec33 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1494 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_436_sample_1 + identifier: + - value: 8f620b3e-2962-49da-bcaf-4ecfd9580923 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A718-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_436_sample_1_subject + identifier: + - value: TCGA-UF-A718-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2135b007-b714-495b-9b30-92010179ec33 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1494 + unit: + coding: *id001 + quantity_collected: + value_decimal: 120 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_436_sample_2 + identifier: + - value: ddeeb19e-1929-488d-8e19-c6212b3b78fb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A718-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_436_sample_2_subject + identifier: + - value: TCGA-UF-A718-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2135b007-b714-495b-9b30-92010179ec33 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_437_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_437_diagnosis_0 + identifier: + - value: 514322a5-47cf-5d99-8ae8-f4466bbad28e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_437 + identifier: + - value: 22ae99b4-52cf-4d20-a068-7457e16919b6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A6IF + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22463 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_437_sample_0 + identifier: + - value: b3a8b960-6807-42ec-b6a8-492d58de2b86 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6IF-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_437_sample_0_subject + identifier: + - value: TCGA-QK-A6IF-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22ae99b4-52cf-4d20-a068-7457e16919b6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 55 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_437_sample_1 + identifier: + - value: bfbfb315-632c-43e7-ae3b-61bcd82b0d3b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6IF-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_437_sample_1_subject + identifier: + - value: TCGA-QK-A6IF-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22ae99b4-52cf-4d20-a068-7457e16919b6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_437_sample_2 + identifier: + - value: 5e77db09-dc35-4cfa-ac78-0f7af0b742ec + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6IF-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_437_sample_2_subject + identifier: + - value: TCGA-QK-A6IF-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22ae99b4-52cf-4d20-a068-7457e16919b6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 55 + unit: + coding: *id001 + quantity_collected: + value_decimal: 70 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_438_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_438_diagnosis_0 + identifier: + - value: 72d80059-302c-57fe-89fa-10045543f0ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_438 + identifier: + - value: 03b57fee-55c7-4873-b7ef-e29abd98863a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A6V1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21730 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_438_sample_0 + identifier: + - value: b2ad9679-048c-43c4-9d78-45638ad5a493 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A6V1-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_438_sample_0_subject + identifier: + - value: TCGA-CN-A6V1-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 03b57fee-55c7-4873-b7ef-e29abd98863a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 141 + unit: + coding: *id001 + quantity_collected: + value_decimal: 170 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_438_sample_1 + identifier: + - value: 8f952c62-2404-484c-b8af-33ce60f4e024 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A6V1-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_438_sample_1_subject + identifier: + - value: TCGA-CN-A6V1-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 03b57fee-55c7-4873-b7ef-e29abd98863a + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 141 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_439_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_439_diagnosis_0 + identifier: + - value: 5606079e-0d29-5f59-acc3-d6de7b479a24 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_439 + identifier: + - value: 3cf77e08-ea34-4091-b242-75c7e35ff699 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A461 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23955 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2004-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_439_sample_0 + identifier: + - value: 76af13f8-fcb3-4324-b8aa-23ea1834c5d2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A461-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_439_sample_0_subject + identifier: + - value: TCGA-CV-A461-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3cf77e08-ea34-4091-b242-75c7e35ff699 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_439_sample_1 + identifier: + - value: af7bb799-b091-45d9-a04e-074bb7840680 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A461-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_439_sample_1_subject + identifier: + - value: TCGA-CV-A461-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3cf77e08-ea34-4091-b242-75c7e35ff699 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 2875 + unit: + coding: *id001 + quantity_collected: + value_decimal: 250 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_439_sample_2 + identifier: + - value: ac4430c7-dbe4-432f-9763-81707431a0f0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A461-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_439_sample_2_subject + identifier: + - value: TCGA-CV-A461-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3cf77e08-ea34-4091-b242-75c7e35ff699 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 2875 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_440_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_440_diagnosis_0 + identifier: + - value: bb2f0211-8bd8-5667-a49f-0e507f10e863 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_440 + identifier: + - value: 815119e3-13c4-4f63-98c7-10a519034a25 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7424 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24775 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1997-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_440_sample_0 + identifier: + - value: 9308d3df-4126-470f-9dae-db9362050c29 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7424-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_440_sample_0_subject + identifier: + - value: TCGA-CV-7424-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 815119e3-13c4-4f63-98c7-10a519034a25 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_440_sample_1 + identifier: + - value: 979324ca-d8fa-4bbd-ad7e-1c663c5a4a9b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7424-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_440_sample_1_subject + identifier: + - value: TCGA-CV-7424-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 815119e3-13c4-4f63-98c7-10a519034a25 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_440_sample_2 + identifier: + - value: 162ba21b-8262-4815-9e65-5b064f0e5885 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7424-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_440_sample_2_subject + identifier: + - value: TCGA-CV-7424-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 815119e3-13c4-4f63-98c7-10a519034a25 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_440_sample_3 + identifier: + - value: 7dafe515-fefb-4656-ab96-b72e09e041f7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7424-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_440_sample_3_subject + identifier: + - value: TCGA-CV-7424-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 815119e3-13c4-4f63-98c7-10a519034a25 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_441_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_441_diagnosis_0 + identifier: + - value: c7db86f3-b6c1-59db-961c-534b91393b19 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_441 + identifier: + - value: af31bf2c-8523-4376-bfa8-e2845848d651 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6010 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19475 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_441_sample_0 + identifier: + - value: cd2a5d45-9bae-4c96-b8dd-7ad079153a49 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6010-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_441_sample_0_subject + identifier: + - value: TCGA-CN-6010-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: af31bf2c-8523-4376-bfa8-e2845848d651 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_441_sample_1 + identifier: + - value: 904e12f8-ab59-4ad8-8096-7b82f9388d70 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6010-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_441_sample_1_subject + identifier: + - value: TCGA-CN-6010-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: af31bf2c-8523-4376-bfa8-e2845848d651 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_441_sample_2 + identifier: + - value: cece12a4-5f68-4a6d-8815-e88495da08f4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6010-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_441_sample_2_subject + identifier: + - value: TCGA-CN-6010-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: af31bf2c-8523-4376-bfa8-e2845848d651 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_442_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_442_diagnosis_0 + identifier: + - value: 0b8731f0-363a-4989-ac32-3ad093d433c4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_442 + identifier: + - value: aac2aae9-ffee-488c-a5eb-6e5f83bdc8ee + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0003031 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_442_sample_0 + identifier: + - value: e44b074f-5e47-4faa-bd94-7375982fbd90 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0003031-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_442_sample_0_subject + identifier: + - value: GENIE-MSK-P-0003031-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: aac2aae9-ffee-488c-a5eb-6e5f83bdc8ee + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_443_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_443_diagnosis_0 + identifier: + - value: b8f93296-f293-4af4-83bd-6ae35aebe59c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_443 + identifier: + - value: f214330c-7401-4ed6-90e0-8c2594a759a1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010368 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_443_sample_0 + identifier: + - value: 094236a4-db5d-4e05-b020-5136ee6f4225 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010368-9817 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_443_sample_0_subject + identifier: + - value: GENIE-DFCI-010368-9817 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f214330c-7401-4ed6-90e0-8c2594a759a1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_444_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_444_diagnosis_0 + identifier: + - value: 693a7e67-099e-5382-b7e2-e70d6d15406f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_444 + identifier: + - value: 9bcf4ed8-bfb4-49aa-a37e-d91325926894 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-6962 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24103 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_444_sample_0 + identifier: + - value: 70b5b27d-3905-40de-8b70-9185cfc49d94 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6962-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_444_sample_0_subject + identifier: + - value: TCGA-CV-6962-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9bcf4ed8-bfb4-49aa-a37e-d91325926894 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_444_sample_1 + identifier: + - value: 5b2faa3f-c96e-42c6-81ce-a356852ea6a6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6962-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_444_sample_1_subject + identifier: + - value: TCGA-CV-6962-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9bcf4ed8-bfb4-49aa-a37e-d91325926894 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_444_sample_2 + identifier: + - value: 73d79c62-61b6-4e72-bc8d-c3fa2a344caf + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6962-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_444_sample_2_subject + identifier: + - value: TCGA-CV-6962-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9bcf4ed8-bfb4-49aa-a37e-d91325926894 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_444_sample_3 + identifier: + - value: 366f8ab0-ddd8-4383-9bc1-96ef342b749c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6962-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_444_sample_3_subject + identifier: + - value: TCGA-CV-6962-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9bcf4ed8-bfb4-49aa-a37e-d91325926894 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_445_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_445_diagnosis_0 + identifier: + - value: 59b73fbd-93ab-5cbb-b052-82d5e66a4c16 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_445 + identifier: + - value: c7df3466-b9a7-4818-883b-d0cd08483570 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-5249 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 13047 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2007-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_445_sample_0 + identifier: + - value: 6697dd71-5a58-4862-b26e-ea16dcc383f2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5249-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_445_sample_0_subject + identifier: + - value: TCGA-CR-5249-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c7df3466-b9a7-4818-883b-d0cd08483570 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_445_sample_1 + identifier: + - value: b72390d2-f19e-493d-9a30-cd81dd232188 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5249-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_445_sample_1_subject + identifier: + - value: TCGA-CR-5249-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c7df3466-b9a7-4818-883b-d0cd08483570 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_446_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_446_diagnosis_0 + identifier: + - value: bad7f79b-abec-4d69-8c30-3abd1a5f31d9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_446 + identifier: + - value: 61f64453-8be1-4d39-a3ff-749d874b2c96 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-UHN-700007 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_446_sample_0 + identifier: + - value: 72155863-300c-4515-962a-d0c332cf5b63 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-UHN-700007-ARC1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_446_sample_0_subject + identifier: + - value: GENIE-UHN-700007-ARC1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 61f64453-8be1-4d39-a3ff-749d874b2c96 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_447_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_447_diagnosis_0 + identifier: + - value: 2707217b-5a4b-404b-97de-921526581d45 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_447 + identifier: + - value: 4d49b9f5-09a0-49de-84f7-0d3441c214f6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-2b4655c3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_447_sample_0 + identifier: + - value: 56e9e0e1-5435-4b6b-93a0-70564fe1aa27 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-2b4655c3-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_447_sample_0_subject + identifier: + - value: GENIE-GRCC-2b4655c3-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4d49b9f5-09a0-49de-84f7-0d3441c214f6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_448_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_448_diagnosis_0 + identifier: + - value: e4e39ca9-5e45-497f-b616-8e4d9edf9431 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_448 + identifier: + - value: 05cc4698-c7a2-4d65-a259-7542164058ea + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-3876b32c + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_448_sample_0 + identifier: + - value: 59d867e0-1111-4114-b47d-39b108eecf06 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-3876b32c-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_448_sample_0_subject + identifier: + - value: GENIE-GRCC-3876b32c-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 05cc4698-c7a2-4d65-a259-7542164058ea + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_449_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_449_diagnosis_0 + identifier: + - value: 39076d27-3e66-4f32-a646-08d8e866bb8c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_449 + identifier: + - value: 9935f385-c860-45b4-aeed-a71f7d1360c9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-5201a20a + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_449_sample_0 + identifier: + - value: 68c9aea7-2d45-4200-b2e5-02aa0ab64d09 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-5201a20a-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_449_sample_0_subject + identifier: + - value: GENIE-GRCC-5201a20a-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9935f385-c860-45b4-aeed-a71f7d1360c9 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_450_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_450_diagnosis_0 + identifier: + - value: 6cba02c0-48e0-4424-964c-a104a6652d07 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_450 + identifier: + - value: 4da985f2-daf8-4d59-8dee-e2bc6041e018 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-007903 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_450_sample_0 + identifier: + - value: fbd21489-29cd-4d9b-8d7c-e04342040edc + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-007903-6035 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_450_sample_0_subject + identifier: + - value: GENIE-DFCI-007903-6035 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4da985f2-daf8-4d59-8dee-e2bc6041e018 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_451_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_451_diagnosis_0 + identifier: + - value: a4332fc7-aee9-497b-99ba-5c1d548a7623 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_451 + identifier: + - value: 5e74a1f6-162f-4a5a-8465-c50e6a2a5e93 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-037277 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_451_sample_0 + identifier: + - value: d2ad484e-58b3-4e29-84e3-a45abb294b3a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-037277-88571 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_451_sample_0_subject + identifier: + - value: GENIE-DFCI-037277-88571 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5e74a1f6-162f-4a5a-8465-c50e6a2a5e93 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_452_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_452_diagnosis_0 + identifier: + - value: 0b894a71-55ca-4246-bdf3-4d36622b203c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_452 + identifier: + - value: 4f699037-52ff-4cda-b97f-a55833d86b8a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0007622 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_452_sample_0 + identifier: + - value: 8b9e009a-6ead-4105-a148-8c8a44be0658 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0007622-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_452_sample_0_subject + identifier: + - value: GENIE-MSK-P-0007622-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4f699037-52ff-4cda-b97f-a55833d86b8a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_453_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_453_diagnosis_0 + identifier: + - value: dcc6b724-3a6f-43bc-9a7a-eb031a031212 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_453 + identifier: + - value: d358b658-b5e0-4561-a8d3-78c05e569d13 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0000433 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_453_sample_0 + identifier: + - value: afcf4bae-7e95-4306-9627-c9a9d6011dfa + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0000433-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_453_sample_0_subject + identifier: + - value: GENIE-MSK-P-0000433-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d358b658-b5e0-4561-a8d3-78c05e569d13 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_454_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_454_diagnosis_0 + identifier: + - value: fa79bd3b-f6c7-48c1-93af-5b6fb08de876 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_454 + identifier: + - value: 7709423b-cfec-4e49-acbc-51c2c7ccf7f2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-003292 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_454_sample_0 + identifier: + - value: a3eaae17-ef1a-442c-93cc-0fd82a8887bf + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-003292-1283 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_454_sample_0_subject + identifier: + - value: GENIE-DFCI-003292-1283 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7709423b-cfec-4e49-acbc-51c2c7ccf7f2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_455_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_455_diagnosis_0 + identifier: + - value: be57683f-0245-4929-89d2-98740dc99b8c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_455 + identifier: + - value: a3e3aab3-93bb-42f6-9a01-f2c9436b699b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-011271 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_455_sample_0 + identifier: + - value: fe032782-a750-46b3-a282-26e110ed063a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-011271-11674 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_455_sample_0_subject + identifier: + - value: GENIE-DFCI-011271-11674 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a3e3aab3-93bb-42f6-9a01-f2c9436b699b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_456_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_456_diagnosis_0 + identifier: + - value: a47bda97-0952-47fa-9a6e-277baa8762a9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_456 + identifier: + - value: 0fef30a9-ce7e-4654-9e35-8d8eb89ace27 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-004713 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_456_sample_0 + identifier: + - value: cc589138-6e86-49ad-8d76-857543c02842 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-004713-938 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_456_sample_0_subject + identifier: + - value: GENIE-DFCI-004713-938 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0fef30a9-ce7e-4654-9e35-8d8eb89ace27 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_457_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_457_diagnosis_0 + identifier: + - value: a4f6276a-b3cc-45f9-9fb8-30edd56ad4ea + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_457 + identifier: + - value: a203ac35-914f-4f4d-816c-2af124257500 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-011620 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_457_sample_0 + identifier: + - value: d697e728-9813-4ff5-83eb-c7d814e07bcc + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-011620-10763 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_457_sample_0_subject + identifier: + - value: GENIE-DFCI-011620-10763 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a203ac35-914f-4f4d-816c-2af124257500 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_458_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_458_diagnosis_0 + identifier: + - value: 192c4be7-66ba-416a-abfb-1a88e63e7be4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_458 + identifier: + - value: 965a1ef7-826f-45ed-a8af-a6ebc4b29815 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-534918 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_458_sample_0 + identifier: + - value: e15f8344-5f7f-4602-b2e3-8fcb0418cb8b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-534918-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_458_sample_0_subject + identifier: + - value: GENIE-VICC-534918-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 965a1ef7-826f-45ed-a8af-a6ebc4b29815 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_459_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_459_diagnosis_0 + identifier: + - value: 1fdf9d03-4341-4aaa-b47a-98f1221816ea + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_459 + identifier: + - value: 8aaae336-eff3-47d9-a50c-0b23904528aa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD3249 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19472 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_459_sample_0 + identifier: + - value: 425f42d0-0349-42bb-9072-cfb0bd97e922 + system: http://crdc.nci.nih.gov/gdc + - value: AD3249_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_459_sample_0_subject + identifier: + - value: AD3249_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8aaae336-eff3-47d9-a50c-0b23904528aa + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_460_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_460_diagnosis_0 + identifier: + - value: 81f6058e-7aef-4ed0-b7c4-a0f1ff8a52b6 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_460 + identifier: + - value: f880a8a9-d4f2-4249-840c-2334e37222a4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-036373 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_460_sample_0 + identifier: + - value: 3b018cb9-12c9-4445-b021-1fc93e0f74c2 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-036373-130403 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_460_sample_0_subject + identifier: + - value: GENIE-DFCI-036373-130403 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f880a8a9-d4f2-4249-840c-2334e37222a4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_461_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_461_diagnosis_0 + identifier: + - value: 1ebf1ce6-31bd-4c8e-b3e0-f70d47cdc527 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_461 + identifier: + - value: f31d8b71-979a-4092-a07f-e2bf0fdac689 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0016351 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_461_sample_0 + identifier: + - value: 90f2519b-17ba-40ad-baee-cb711b306a91 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0016351-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_461_sample_0_subject + identifier: + - value: GENIE-MSK-P-0016351-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f31d8b71-979a-4092-a07f-e2bf0fdac689 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_462_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_462_diagnosis_0 + identifier: + - value: 0b96cae3-d332-4e5e-ba59-e0a6bc6573df + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_462 + identifier: + - value: 9e3ddcea-f01d-425b-9669-99531e27b27a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0017105 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_462_sample_0 + identifier: + - value: ba279369-073d-4976-8439-3a318c0f0fc3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0017105-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_462_sample_0_subject + identifier: + - value: GENIE-MSK-P-0017105-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9e3ddcea-f01d-425b-9669-99531e27b27a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_463_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_463_diagnosis_0 + identifier: + - value: f3270d37-2d06-4867-973e-54e8ea28208b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_463 + identifier: + - value: 193ba68a-b208-4f4f-ab46-e4cf351a5edf + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002787 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_463_sample_0 + identifier: + - value: 3eb1f15d-003c-42bc-8832-ea364ee8931b + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002787-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_463_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002787-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 193ba68a-b208-4f4f-ab46-e4cf351a5edf + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_464_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_464_diagnosis_0 + identifier: + - value: c0bc6849-2b35-4465-9d65-38c3a21a9a25 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_464 + identifier: + - value: 5227e135-4c93-4df5-aa5a-04138eaf1af6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0019226 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_464_sample_0 + identifier: + - value: b33d58a0-8855-42ac-baaa-0a1e961307f4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0019226-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_464_sample_0_subject + identifier: + - value: GENIE-MSK-P-0019226-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5227e135-4c93-4df5-aa5a-04138eaf1af6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_465_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_465_diagnosis_0 + identifier: + - value: cee28001-9ebf-46a7-b387-e932076e5df8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_465 + identifier: + - value: 09f09710-dde2-414e-a315-be5d4491c839 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010817 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_465_sample_0 + identifier: + - value: 08a27a81-561d-41f1-9d99-6266c1f230c9 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010817-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_465_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010817-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 09f09710-dde2-414e-a315-be5d4491c839 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_466_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_466_diagnosis_0 + identifier: + - value: de59133c-2442-490c-9f22-057c8a47ff70 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_466 + identifier: + - value: d79f2526-8e1b-46f0-8c4b-42d08e6c80c1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008518 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_466_sample_0 + identifier: + - value: f4e28471-79a4-456e-bba8-db331560bdb0 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008518-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_466_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008518-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d79f2526-8e1b-46f0-8c4b-42d08e6c80c1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_467_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_467_diagnosis_0 + identifier: + - value: 0b151db5-f3df-4cc8-9bf3-049308634116 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_467 + identifier: + - value: ed3f424f-8652-4e8b-800a-2820df70685f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001794 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_467_sample_0 + identifier: + - value: 2da79fb4-bd1b-4518-a6a2-6159251d65fb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001794-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_467_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001794-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ed3f424f-8652-4e8b-800a-2820df70685f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_468_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_468_diagnosis_0 + identifier: + - value: cf973339-e31d-4fb3-833e-f954634d95ee + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_468 + identifier: + - value: 7f54c1b8-1dc4-4de5-a074-e2e1a8a012fa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0014965 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_468_sample_0 + identifier: + - value: 1bd46cb2-e563-4a48-a36e-ea4f7a15173f + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0014965-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_468_sample_0_subject + identifier: + - value: GENIE-MSK-P-0014965-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7f54c1b8-1dc4-4de5-a074-e2e1a8a012fa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_469_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_469_diagnosis_0 + identifier: + - value: 9b998038-9a23-4348-a5f7-e2d3126e118c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_469 + identifier: + - value: df5f7166-08b1-4b89-b4bc-9707f83a6029 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD14936 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21177 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_469_sample_0 + identifier: + - value: fc50dce3-ca12-4a52-a8fd-27dcd3887746 + system: http://crdc.nci.nih.gov/gdc + - value: AD14936_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_469_sample_0_subject + identifier: + - value: AD14936_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: df5f7166-08b1-4b89-b4bc-9707f83a6029 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_470_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_470_diagnosis_0 + identifier: + - value: 4176108f-948d-5715-afbb-cc21f3cbfaf5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_470 + identifier: + - value: 291b069c-9dde-4e1e-8430-85146bc94338 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5363 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17635 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2007-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_470_sample_0 + identifier: + - value: 591e99ec-46f9-442d-ac20-745dccc8a52b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5363-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_470_sample_0_subject + identifier: + - value: TCGA-CN-5363-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 291b069c-9dde-4e1e-8430-85146bc94338 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_470_sample_1 + identifier: + - value: d0161f8c-9c53-47ad-895c-40d1be3a814e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5363-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_470_sample_1_subject + identifier: + - value: TCGA-CN-5363-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 291b069c-9dde-4e1e-8430-85146bc94338 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_470_sample_2 + identifier: + - value: 5e4e1e21-8016-4e27-8f72-2411714203e8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5363-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_470_sample_2_subject + identifier: + - value: TCGA-CN-5363-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 291b069c-9dde-4e1e-8430-85146bc94338 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_471_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_471_diagnosis_0 + identifier: + - value: 43cceeb5-008a-58cb-b219-34c3ac43e86f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_471 + identifier: + - value: 76214b90-c323-4fdc-92f4-1180abdb1380 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A497 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23310 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_471_sample_0 + identifier: + - value: 882c6ec3-1f56-43c3-8a41-da060f9f5ee1 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A497-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_471_sample_0_subject + identifier: + - value: TCGA-CN-A497-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 76214b90-c323-4fdc-92f4-1180abdb1380 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 450 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_471_sample_1 + identifier: + - value: bea32bd5-4068-4351-994e-09b3bf819ebb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A497-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_471_sample_1_subject + identifier: + - value: TCGA-CN-A497-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 76214b90-c323-4fdc-92f4-1180abdb1380 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 450 + unit: + coding: *id001 + quantity_collected: + value_decimal: 180 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_472_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_472_diagnosis_0 + identifier: + - value: 28f3f8b9-df0c-5c03-8414-89640fa631c5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_472 + identifier: + - value: 59a7d695-cb0c-47b8-ba9d-ca52ca2cfa7d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-H7-A76A + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20946 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_472_sample_0 + identifier: + - value: 78229167-1f08-416d-be98-74f757610349 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A76A-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_472_sample_0_subject + identifier: + - value: TCGA-H7-A76A-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 59a7d695-cb0c-47b8-ba9d-ca52ca2cfa7d + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 58 + unit: + coding: *id001 + quantity_collected: + value_decimal: 510 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_472_sample_1 + identifier: + - value: 148ec5a3-19ed-4949-bf37-9bc4e6203966 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A76A-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_472_sample_1_subject + identifier: + - value: TCGA-H7-A76A-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 59a7d695-cb0c-47b8-ba9d-ca52ca2cfa7d + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 58 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_472_sample_2 + identifier: + - value: 452e53e7-b219-4ba7-b8ab-870e1ba4423b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-H7-A76A-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_472_sample_2_subject + identifier: + - value: TCGA-H7-A76A-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 59a7d695-cb0c-47b8-ba9d-ca52ca2cfa7d + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_473_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_473_diagnosis_0 + identifier: + - value: b8812861-0e19-58f0-bccf-667970cdb04c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_473 + identifier: + - value: ed6ac43c-d921-4342-aeec-9ff8d8a31919 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7399 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22182 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_473_sample_0 + identifier: + - value: 3dd4255a-7359-4b51-8a0b-44d9e249956b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7399-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_473_sample_0_subject + identifier: + - value: TCGA-CR-7399-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ed6ac43c-d921-4342-aeec-9ff8d8a31919 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_473_sample_1 + identifier: + - value: 05c3d8a0-47a2-44b2-b0c3-144ec0cb2673 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7399-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_473_sample_1_subject + identifier: + - value: TCGA-CR-7399-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ed6ac43c-d921-4342-aeec-9ff8d8a31919 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_474_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_474_diagnosis_0 + identifier: + - value: 843f33f9-e390-52bc-90c8-fba0a4557916 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_474 + identifier: + - value: 12d94c6e-323f-450b-b510-f2ab4671e0fa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A7JV + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22985 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_474_sample_0 + identifier: + - value: c312a7a4-ba29-49a9-b4dc-876505a6a6c4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JV-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_474_sample_0_subject + identifier: + - value: TCGA-UF-A7JV-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12d94c6e-323f-450b-b510-f2ab4671e0fa + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_474_sample_1 + identifier: + - value: eed0dcf3-36a2-4890-bb02-e8b56ba4d8d8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JV-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_474_sample_1_subject + identifier: + - value: TCGA-UF-A7JV-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12d94c6e-323f-450b-b510-f2ab4671e0fa + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 835 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_474_sample_2 + identifier: + - value: a1d62ba6-696c-4693-9067-d4226a4e6316 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JV-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_474_sample_2_subject + identifier: + - value: TCGA-UF-A7JV-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 12d94c6e-323f-450b-b510-f2ab4671e0fa + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 835 + unit: + coding: *id001 + quantity_collected: + value_decimal: 90 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_475_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_475_diagnosis_0 + identifier: + - value: b1c3bd39-9f13-5dba-aeeb-86271bf64b8d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_475 + identifier: + - value: 4b4247e2-4446-44f5-8573-4cea8bf69f8e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7242 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22136 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_475_sample_0 + identifier: + - value: 4fdddf85-30de-4666-89d2-0683e9264d6d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7242-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_475_sample_0_subject + identifier: + - value: TCGA-CV-7242-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b4247e2-4446-44f5-8573-4cea8bf69f8e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_475_sample_1 + identifier: + - value: 6b4b146e-e6c5-454d-9c4f-66a6f851c3fe + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7242-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_475_sample_1_subject + identifier: + - value: TCGA-CV-7242-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b4247e2-4446-44f5-8573-4cea8bf69f8e + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_475_sample_2 + identifier: + - value: a45efd70-9bee-4c18-82b1-666d2c1eb781 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7242-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_475_sample_2_subject + identifier: + - value: TCGA-CV-7242-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b4247e2-4446-44f5-8573-4cea8bf69f8e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_475_sample_3 + identifier: + - value: f9dea7a5-e9d2-48a6-bbc1-c5c1f8e7ee67 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7242-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_475_sample_3_subject + identifier: + - value: TCGA-CV-7242-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b4247e2-4446-44f5-8573-4cea8bf69f8e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_476_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_476_diagnosis_0 + identifier: + - value: de41284b-65f5-592e-99bb-9157a9509c36 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_476 + identifier: + - value: dbdeb4ca-f67c-4d89-af60-88b425ebe461 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-T3-A92M + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19247 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_476_sample_0 + identifier: + - value: 86c72a0c-24c8-4d55-9f87-6b7198a10890 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T3-A92M-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_476_sample_0_subject + identifier: + - value: TCGA-T3-A92M-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbdeb4ca-f67c-4d89-af60-88b425ebe461 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 147 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_476_sample_1 + identifier: + - value: cdefaeb2-3a2b-4094-b25e-0c509b62c13b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T3-A92M-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_476_sample_1_subject + identifier: + - value: TCGA-T3-A92M-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbdeb4ca-f67c-4d89-af60-88b425ebe461 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_476_sample_2 + identifier: + - value: d22843cb-8a14-4592-b339-a04cf1514205 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-T3-A92M-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_476_sample_2_subject + identifier: + - value: TCGA-T3-A92M-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dbdeb4ca-f67c-4d89-af60-88b425ebe461 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 147 + unit: + coding: *id001 + quantity_collected: + value_decimal: 240 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_477_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_477_diagnosis_0 + identifier: + - value: 6bbf8ace-0b17-57e5-bf9e-2c164cb28e53 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_477 + identifier: + - value: 795677d4-dc60-4ebd-a9df-e88713e5a4aa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-F7-A50I + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26373 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_477_sample_0 + identifier: + - value: 5eb175ff-1b47-463a-8f16-4b59914457bc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A50I-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_477_sample_0_subject + identifier: + - value: TCGA-F7-A50I-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 795677d4-dc60-4ebd-a9df-e88713e5a4aa + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 335 + unit: + coding: *id001 + quantity_collected: + value_decimal: 90 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_477_sample_1 + identifier: + - value: 384902a7-fa03-4083-9baf-7ce114694c9d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A50I-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_477_sample_1_subject + identifier: + - value: TCGA-F7-A50I-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 795677d4-dc60-4ebd-a9df-e88713e5a4aa + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_477_sample_2 + identifier: + - value: ccd8f2ed-5a6a-460f-b692-ee7d78e29b18 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A50I-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_477_sample_2_subject + identifier: + - value: TCGA-F7-A50I-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 795677d4-dc60-4ebd-a9df-e88713e5a4aa + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 335 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_478_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_478_diagnosis_0 + identifier: + - value: c9ea5a2b-8b14-5745-b9c3-c93c9abe468f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_478 + identifier: + - value: 9e3e8014-04d4-40d8-b2df-53c770e01df2 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-A45O + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20868 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1994-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_478_sample_0 + identifier: + - value: fce64b88-8be6-4710-83be-18c9afdf13ed + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45O-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_478_sample_0_subject + identifier: + - value: TCGA-CV-A45O-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9e3e8014-04d4-40d8-b2df-53c770e01df2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 6651 + unit: + coding: *id001 + quantity_collected: + value_decimal: 240 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_478_sample_1 + identifier: + - value: ec7fe5e6-74af-4bd2-9ecb-8e302f763b22 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45O-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_478_sample_1_subject + identifier: + - value: TCGA-CV-A45O-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9e3e8014-04d4-40d8-b2df-53c770e01df2 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 6651 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_478_sample_2 + identifier: + - value: 77b774a4-9456-4907-86e6-9ff2dd87b8fd + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-A45O-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_478_sample_2_subject + identifier: + - value: TCGA-CV-A45O-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9e3e8014-04d4-40d8-b2df-53c770e01df2 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_479_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_479_diagnosis_0 + identifier: + - value: 9be1751f-17dd-5748-a489-1b4eb3235e17 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_479 + identifier: + - value: fd7e2226-8086-4a56-867b-6457b87a7fed + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-MZ-A5BI + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19500 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_479_sample_0 + identifier: + - value: f1e46036-7b4f-4cca-a150-f2d8e599fdf7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MZ-A5BI-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_479_sample_0_subject + identifier: + - value: TCGA-MZ-A5BI-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fd7e2226-8086-4a56-867b-6457b87a7fed + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1723 + unit: + coding: *id001 + quantity_collected: + value_decimal: 550 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_479_sample_1 + identifier: + - value: c226c7c5-64e6-4790-a420-c2f4e0196453 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MZ-A5BI-10C + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_479_sample_1_subject + identifier: + - value: TCGA-MZ-A5BI-10C + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fd7e2226-8086-4a56-867b-6457b87a7fed + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1883 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_480_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_480_diagnosis_0 + identifier: + - value: dac87ff6-12f3-553f-a6cb-fae679002ff0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_480 + identifier: + - value: b64bfca1-033c-4501-a900-103ac105c084 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4722 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22299 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_480_sample_0 + identifier: + - value: 6e767fc9-0f5a-49ec-999a-cda2daeba6ff + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4722-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_480_sample_0_subject + identifier: + - value: TCGA-CN-4722-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b64bfca1-033c-4501-a900-103ac105c084 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_480_sample_1 + identifier: + - value: 47e7b839-bde5-4b66-98da-7ed6e3e7c29b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4722-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_480_sample_1_subject + identifier: + - value: TCGA-CN-4722-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b64bfca1-033c-4501-a900-103ac105c084 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_480_sample_2 + identifier: + - value: 60c8633c-16f9-4066-8aad-311b04b935e5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4722-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_480_sample_2_subject + identifier: + - value: TCGA-CN-4722-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b64bfca1-033c-4501-a900-103ac105c084 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_481_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_481_diagnosis_0 + identifier: + - value: 7bbdbf5a-baf7-55b4-bd8d-89e213744a26 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_481 + identifier: + - value: 3e49a2b8-9b2c-4d15-9773-24df8b4ab2fd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A6VC + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22865 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_481_sample_0 + identifier: + - value: d278f388-2a5f-407f-886d-961272ca28eb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6VC-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_481_sample_0_subject + identifier: + - value: TCGA-QK-A6VC-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3e49a2b8-9b2c-4d15-9773-24df8b4ab2fd + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_481_sample_1 + identifier: + - value: dbea2268-ac62-4ab7-aa7d-86f029fcb2df + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6VC-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_481_sample_1_subject + identifier: + - value: TCGA-QK-A6VC-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3e49a2b8-9b2c-4d15-9773-24df8b4ab2fd + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 24 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_481_sample_2 + identifier: + - value: 76240522-a39e-48c7-80e0-241277fdb705 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6VC-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_481_sample_2_subject + identifier: + - value: TCGA-QK-A6VC-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3e49a2b8-9b2c-4d15-9773-24df8b4ab2fd + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 24 + unit: + coding: *id001 + quantity_collected: + value_decimal: 210 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_482_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_482_diagnosis_0 + identifier: + - value: 8bd7b118-92b1-4443-8753-f779c82ef116 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_482 + identifier: + - value: a4dcc980-d79c-4b69-a705-79dbd1abc892 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-035615 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_482_sample_0 + identifier: + - value: 151f2c1e-f448-4fa5-9b61-81dc5c339f58 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-035615-74950 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_482_sample_0_subject + identifier: + - value: GENIE-DFCI-035615-74950 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a4dcc980-d79c-4b69-a705-79dbd1abc892 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_483_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_483_diagnosis_0 + identifier: + - value: 4a037aae-de5b-5ac6-875f-b86b71ff50ee + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_483 + identifier: + - value: c7353d6a-82a2-4a0d-8cd4-8c8957943edb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-4078 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 30480 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2003-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_483_sample_0 + identifier: + - value: 2027ede3-13f5-40f6-bef6-16704981d676 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-4078-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_483_sample_0_subject + identifier: + - value: TCGA-BA-4078-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c7353d6a-82a2-4a0d-8cd4-8c8957943edb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_483_sample_1 + identifier: + - value: 3423d96f-4c5a-40f7-8e66-3dd4b9818f52 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-4078-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_483_sample_1_subject + identifier: + - value: TCGA-BA-4078-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c7353d6a-82a2-4a0d-8cd4-8c8957943edb + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_483_sample_2 + identifier: + - value: 25b0ae1d-2add-49b9-a5ae-99702a5c48f4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-4078-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_483_sample_2_subject + identifier: + - value: TCGA-BA-4078-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c7353d6a-82a2-4a0d-8cd4-8c8957943edb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_484_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_484_diagnosis_0 + identifier: + - value: bddca644-5ced-5789-8d31-c00df9f776ad + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_484 + identifier: + - value: f04f1c1c-6d6d-4a2b-ba88-110b08fcc596 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-A74Q + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24702 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_484_sample_0 + identifier: + - value: c03b3dfa-7b9b-4a21-9274-d174bc14440b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A74Q-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_484_sample_0_subject + identifier: + - value: TCGA-D6-A74Q-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f04f1c1c-6d6d-4a2b-ba88-110b08fcc596 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 108 + unit: + coding: *id001 + quantity_collected: + value_decimal: 80 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_484_sample_1 + identifier: + - value: 343c1ea3-2785-465f-b01a-2d609b486ef9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A74Q-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_484_sample_1_subject + identifier: + - value: TCGA-D6-A74Q-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f04f1c1c-6d6d-4a2b-ba88-110b08fcc596 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 108 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_484_sample_2 + identifier: + - value: d9095c8b-414f-41d4-a478-ee54d2728762 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A74Q-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_484_sample_2_subject + identifier: + - value: TCGA-D6-A74Q-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f04f1c1c-6d6d-4a2b-ba88-110b08fcc596 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_485_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_485_diagnosis_0 + identifier: + - value: 9e0b865b-296f-481f-8bc2-7bfe4642d805 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_485 + identifier: + - value: 9c78774c-c0c4-46c9-85ab-c05879522195 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0001912 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_485_sample_0 + identifier: + - value: 271c4064-6b2e-4971-853f-e3f2a1cdd74a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0001912-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_485_sample_0_subject + identifier: + - value: GENIE-MSK-P-0001912-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9c78774c-c0c4-46c9-85ab-c05879522195 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_486_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_486_diagnosis_0 + identifier: + - value: 6dd63ec3-e88a-4da9-be07-0d11a1768dbf + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_486 + identifier: + - value: e8f539ba-1d6d-420d-aab7-257db14e6c72 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0004416 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_486_sample_0 + identifier: + - value: 34487c7a-5f9a-41b0-8ced-d7c2ce3653e2 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0004416-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_486_sample_0_subject + identifier: + - value: GENIE-MSK-P-0004416-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: e8f539ba-1d6d-420d-aab7-257db14e6c72 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_487_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_487_diagnosis_0 + identifier: + - value: f9a0b1dd-a13b-4a14-ac22-c9570e02ca60 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_487 + identifier: + - value: 5b3d368b-571b-4f75-8dc7-15ef276c44a0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008792 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_487_sample_0 + identifier: + - value: b882dbe8-5494-4092-8bad-ccca6b119775 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008792-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_487_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008792-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5b3d368b-571b-4f75-8dc7-15ef276c44a0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_488_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_488_diagnosis_0 + identifier: + - value: 310c112e-7e2f-4987-a515-fe213ae70986 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_488 + identifier: + - value: 9f7594e2-b871-400f-877e-c04a3782a8fb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002198 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_488_sample_0 + identifier: + - value: b9d46cb7-1679-4998-853f-03e5827cbb53 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002198-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_488_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002198-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9f7594e2-b871-400f-877e-c04a3782a8fb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_489_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_489_diagnosis_0 + identifier: + - value: f543ba05-0134-4222-bc49-da336358e2e0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_489 + identifier: + - value: 379b1838-f8bc-45e8-a01f-7ed06047a186 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0005862 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_489_sample_0 + identifier: + - value: fbb548d6-a035-43c3-99a4-7fb2892ade49 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0005862-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_489_sample_0_subject + identifier: + - value: GENIE-MSK-P-0005862-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 379b1838-f8bc-45e8-a01f-7ed06047a186 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_490_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_490_diagnosis_0 + identifier: + - value: e3d5bf4e-2856-5604-a086-3e4464a68c05 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_490 + identifier: + - value: 3bd2fcee-5b16-49f3-a717-f1e106bbc12f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A7JF + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 29468 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_490_sample_0 + identifier: + - value: 7ce8968e-f693-4fa2-945a-0cea27c96ede + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JF-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_490_sample_0_subject + identifier: + - value: TCGA-UF-A7JF-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3bd2fcee-5b16-49f3-a717-f1e106bbc12f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1219 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_490_sample_1 + identifier: + - value: f4e12699-7e71-42ba-994a-c3a9a71a95cb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JF-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_490_sample_1_subject + identifier: + - value: TCGA-UF-A7JF-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3bd2fcee-5b16-49f3-a717-f1e106bbc12f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1219 + unit: + coding: *id001 + quantity_collected: + value_decimal: 70 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_490_sample_2 + identifier: + - value: f4cf2a66-8872-41ee-8270-296d5f76265f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JF-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_490_sample_2_subject + identifier: + - value: TCGA-UF-A7JF-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3bd2fcee-5b16-49f3-a717-f1e106bbc12f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_491_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_491_diagnosis_0 + identifier: + - value: 45ebf5cb-a072-582b-8ace-7cd198806bc2 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_491 + identifier: + - value: 829b41b1-693b-4f7f-a5c2-68c14b079aae + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-F7-7848 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17251 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_491_sample_0 + identifier: + - value: f7831fa0-1f1d-4623-aba0-8117b925a1ee + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-7848-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_491_sample_0_subject + identifier: + - value: TCGA-F7-7848-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 829b41b1-693b-4f7f-a5c2-68c14b079aae + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_491_sample_1 + identifier: + - value: b99fa26a-da90-4b98-bea0-f0c71a1b6ea3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-7848-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_491_sample_1_subject + identifier: + - value: TCGA-F7-7848-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 829b41b1-693b-4f7f-a5c2-68c14b079aae + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_491_sample_2 + identifier: + - value: 8aa78dee-bc22-4d4b-86d6-60fb80358da8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-7848-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_491_sample_2_subject + identifier: + - value: TCGA-F7-7848-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 829b41b1-693b-4f7f-a5c2-68c14b079aae + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_492_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_492_diagnosis_0 + identifier: + - value: cceca036-354c-59e4-ad7a-886865aada46 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_492 + identifier: + - value: ae2051a3-f851-4cb3-af18-029f4574b179 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7245 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22646 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_492_sample_0 + identifier: + - value: aaa6607c-e333-4f99-b1dc-390c3cad4f1b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7245-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_492_sample_0_subject + identifier: + - value: TCGA-CV-7245-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ae2051a3-f851-4cb3-af18-029f4574b179 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_492_sample_1 + identifier: + - value: d455327a-a947-4a67-8fb5-44438abe5976 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7245-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_492_sample_1_subject + identifier: + - value: TCGA-CV-7245-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ae2051a3-f851-4cb3-af18-029f4574b179 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_492_sample_2 + identifier: + - value: f0684e03-2d91-4e9b-9d11-a3063ccc2f34 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7245-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_492_sample_2_subject + identifier: + - value: TCGA-CV-7245-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ae2051a3-f851-4cb3-af18-029f4574b179 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_492_sample_3 + identifier: + - value: c8ac9749-82ff-4348-8d91-5ce677697a15 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7245-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_492_sample_3_subject + identifier: + - value: TCGA-CV-7245-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ae2051a3-f851-4cb3-af18-029f4574b179 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_493_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_493_diagnosis_0 + identifier: + - value: 7747a88f-1a9b-5833-9442-af0b1350bb4f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_493 + identifier: + - value: 714496c5-d221-4397-9c5a-cd2d22603e6f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6013 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20703 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_493_sample_0 + identifier: + - value: d018cd44-6b01-44f2-9181-81153225aab8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6013-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_493_sample_0_subject + identifier: + - value: TCGA-CN-6013-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 714496c5-d221-4397-9c5a-cd2d22603e6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_493_sample_1 + identifier: + - value: 8b510bc8-7b3c-4861-9a40-c2c30b7099e0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6013-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_493_sample_1_subject + identifier: + - value: TCGA-CN-6013-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 714496c5-d221-4397-9c5a-cd2d22603e6f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_493_sample_2 + identifier: + - value: c0c84016-117e-498c-9ed9-52e279e89e33 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6013-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_493_sample_2_subject + identifier: + - value: TCGA-CN-6013-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 714496c5-d221-4397-9c5a-cd2d22603e6f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_494_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_494_diagnosis_0 + identifier: + - value: 8764fb2b-e701-53db-b137-03efa2c52637 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_494 + identifier: + - value: cb78efb3-bc29-4de7-9128-fdc4f9539b48 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A6DI + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22857 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_494_sample_0 + identifier: + - value: e7a7e296-3f1b-49f5-bbaa-082f918d080d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DI-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_494_sample_0_subject + identifier: + - value: TCGA-BA-A6DI-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cb78efb3-bc29-4de7-9128-fdc4f9539b48 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 414 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_494_sample_1 + identifier: + - value: 7b56068d-21e9-4879-b747-c99943e40e50 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DI-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_494_sample_1_subject + identifier: + - value: TCGA-BA-A6DI-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cb78efb3-bc29-4de7-9128-fdc4f9539b48 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_494_sample_2 + identifier: + - value: b0d4b16c-cc81-405f-83a1-de57cb488166 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A6DI-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_494_sample_2_subject + identifier: + - value: TCGA-BA-A6DI-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cb78efb3-bc29-4de7-9128-fdc4f9539b48 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 414 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_495_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_495_diagnosis_0 + identifier: + - value: 1fa242e0-09fa-5f9b-b6ec-b07d25fd21cd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_495 + identifier: + - value: 220d75ae-c94b-473a-a988-ac40c15fa219 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A6SX + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24715 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2005-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_495_sample_0 + identifier: + - value: cc710f34-9fb5-4474-84df-5427b59aa062 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6SX-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_495_sample_0_subject + identifier: + - value: TCGA-P3-A6SX-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 220d75ae-c94b-473a-a988-ac40c15fa219 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 2855 + unit: + coding: *id001 + quantity_collected: + value_decimal: 50 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_495_sample_1 + identifier: + - value: ae3f666a-0c18-41c1-b00e-90cd85a2f987 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6SX-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_495_sample_1_subject + identifier: + - value: TCGA-P3-A6SX-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 220d75ae-c94b-473a-a988-ac40c15fa219 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 2855 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_495_sample_2 + identifier: + - value: 65b091e0-fd47-4f4c-87f1-b2ba9c2766c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A6SX-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_495_sample_2_subject + identifier: + - value: TCGA-P3-A6SX-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 220d75ae-c94b-473a-a988-ac40c15fa219 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_496_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_496_diagnosis_0 + identifier: + - value: fd9653a3-00f4-593c-a8e5-81ed124ee898 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_496 + identifier: + - value: 677c9d22-e518-43ab-9668-a606c35a6eeb + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-AA3J + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25469 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Basaloid squamous cell carcinoma + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8083/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_496_sample_0 + identifier: + - value: b67c34c3-8e4e-41cc-865d-43ee8c9d3d78 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-AA3J-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_496_sample_0_subject + identifier: + - value: TCGA-QK-AA3J-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 677c9d22-e518-43ab-9668-a606c35a6eeb + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 15 + unit: + coding: *id001 + quantity_collected: + value_decimal: 10 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_496_sample_1 + identifier: + - value: 410b2727-8446-41b1-92b9-42671d118a39 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-AA3J-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_496_sample_1_subject + identifier: + - value: TCGA-QK-AA3J-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 677c9d22-e518-43ab-9668-a606c35a6eeb + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_496_sample_2 + identifier: + - value: 6d2f2d82-2fa5-44ea-a714-85c05b5bd255 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-AA3J-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_496_sample_2_subject + identifier: + - value: TCGA-QK-AA3J-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 677c9d22-e518-43ab-9668-a606c35a6eeb + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 15 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_497_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_497_diagnosis_0 + identifier: + - value: f904a635-80a1-579a-8f1f-0aa288492b45 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_497 + identifier: + - value: a2d42990-747c-4618-88dd-e2dece8e566f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A8YP + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18355 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_497_sample_0 + identifier: + - value: a9ebdedd-056f-4bc1-abc2-7089544a1549 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A8YP-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_497_sample_0_subject + identifier: + - value: TCGA-BA-A8YP-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a2d42990-747c-4618-88dd-e2dece8e566f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_497_sample_1 + identifier: + - value: 4a339708-153a-4780-a265-70557765a754 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A8YP-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_497_sample_1_subject + identifier: + - value: TCGA-BA-A8YP-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a2d42990-747c-4618-88dd-e2dece8e566f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 65 + unit: + coding: *id001 + quantity_collected: + value_decimal: 290 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_497_sample_2 + identifier: + - value: e62166c3-871d-4b0f-999a-4f033d7cb6c7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A8YP-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_497_sample_2_subject + identifier: + - value: TCGA-BA-A8YP-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a2d42990-747c-4618-88dd-e2dece8e566f + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 65 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_498_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_498_diagnosis_0 + identifier: + - value: 9808f3d0-16f0-519d-8e0a-9061968bc749 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_498 + identifier: + - value: 69efde94-a9f9-49ff-9c82-028c35940eda + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6023 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26769 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_498_sample_0 + identifier: + - value: ae1a6096-8d51-482a-8c44-cbfdc7dd6458 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6023-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_498_sample_0_subject + identifier: + - value: TCGA-CN-6023-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 69efde94-a9f9-49ff-9c82-028c35940eda + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_498_sample_1 + identifier: + - value: 0bc27973-621c-4011-bcbd-3b7f3464389e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6023-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_498_sample_1_subject + identifier: + - value: TCGA-CN-6023-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 69efde94-a9f9-49ff-9c82-028c35940eda + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_498_sample_2 + identifier: + - value: 5e42be68-8865-4c69-8684-0f6e5c6c9b94 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6023-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_498_sample_2_subject + identifier: + - value: TCGA-CN-6023-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 69efde94-a9f9-49ff-9c82-028c35940eda + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_499_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_499_diagnosis_0 + identifier: + - value: a276fc76-237c-5574-9fc6-4b309ce35829 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_499 + identifier: + - value: 0871333c-1088-4af1-a365-12256643c5bd + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-6935 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24799 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1999-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_499_sample_0 + identifier: + - value: 76de8a78-90b8-4928-8dc1-bf3b8157382f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6935-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_499_sample_0_subject + identifier: + - value: TCGA-CV-6935-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0871333c-1088-4af1-a365-12256643c5bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_499_sample_1 + identifier: + - value: 37f4a944-d427-4f41-9d27-982a910103e8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6935-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_499_sample_1_subject + identifier: + - value: TCGA-CV-6935-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0871333c-1088-4af1-a365-12256643c5bd + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_499_sample_2 + identifier: + - value: 05aa5c47-cbde-491e-b8d7-a60cfe1ca2d9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6935-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_499_sample_2_subject + identifier: + - value: TCGA-CV-6935-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0871333c-1088-4af1-a365-12256643c5bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_499_sample_3 + identifier: + - value: 6883e88c-05a5-4ae7-a43f-40d4f35a3a2d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-6935-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_499_sample_3_subject + identifier: + - value: TCGA-CV-6935-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0871333c-1088-4af1-a365-12256643c5bd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_500_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_500_diagnosis_0 + identifier: + - value: 3bd2d2d4-7d4a-51f3-bfaf-4153b96110ae + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_500 + identifier: + - value: 180036a2-3b56-405e-a1fe-d5932517b6c7 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-5443 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23287 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2004-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_500_sample_0 + identifier: + - value: f70fece0-2fb1-4d8f-955b-7b9bbfeb9755 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5443-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_500_sample_0_subject + identifier: + - value: TCGA-CV-5443-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 180036a2-3b56-405e-a1fe-d5932517b6c7 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_500_sample_1 + identifier: + - value: 746322c7-fe75-4b9f-9309-93e9cfa4cb5a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5443-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_500_sample_1_subject + identifier: + - value: TCGA-CV-5443-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 180036a2-3b56-405e-a1fe-d5932517b6c7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_500_sample_2 + identifier: + - value: 4863312a-043e-418e-812d-2ae2a1f66f29 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-5443-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_500_sample_2_subject + identifier: + - value: TCGA-CV-5443-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 180036a2-3b56-405e-a1fe-d5932517b6c7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_501_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_501_diagnosis_0 + identifier: + - value: dd691506-83cb-50c1-ae0a-2583d57079d3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_501 + identifier: + - value: a3d89882-6d5b-497a-a9e4-a8b8908c3ff4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A499 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21971 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_501_sample_0 + identifier: + - value: 7d93ba42-9e87-4a6c-8b0d-6f185645a90a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A499-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_501_sample_0_subject + identifier: + - value: TCGA-CN-A499-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a3d89882-6d5b-497a-a9e4-a8b8908c3ff4 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 293 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_501_sample_1 + identifier: + - value: 9ca906ce-18f9-41c5-afcc-353b26fdebaa + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A499-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_501_sample_1_subject + identifier: + - value: TCGA-CN-A499-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a3d89882-6d5b-497a-a9e4-a8b8908c3ff4 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 293 + unit: + coding: *id001 + quantity_collected: + value_decimal: 130 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_502_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_502_diagnosis_0 + identifier: + - value: 4d192f26-a2c4-537b-b8b5-1473a759882c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_502 + identifier: + - value: 82c47f60-b863-45f9-82dc-72d89753f4b1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A7J9 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 27459 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_502_sample_0 + identifier: + - value: 5be42d60-80c3-486f-8717-801fec0c89d3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7J9-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_502_sample_0_subject + identifier: + - value: TCGA-UF-A7J9-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 82c47f60-b863-45f9-82dc-72d89753f4b1 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_502_sample_1 + identifier: + - value: fbceb407-e7f8-4942-8689-854f8999672c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7J9-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_502_sample_1_subject + identifier: + - value: TCGA-UF-A7J9-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 82c47f60-b863-45f9-82dc-72d89753f4b1 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 945 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_502_sample_2 + identifier: + - value: 5df6c457-baef-451d-b1cf-eb7fa6adc602 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7J9-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_502_sample_2_subject + identifier: + - value: TCGA-UF-A7J9-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 82c47f60-b863-45f9-82dc-72d89753f4b1 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 945 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_503_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_503_diagnosis_0 + identifier: + - value: 812129f0-3b47-5ede-9062-237e0c0be7c5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_503 + identifier: + - value: 8970f713-4a7a-4125-892c-6a34139371d8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-5555 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19956 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_503_sample_0 + identifier: + - value: 7c56b9e6-8fd8-4d39-92f0-a24c80270dda + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5555-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_503_sample_0_subject + identifier: + - value: TCGA-BA-5555-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8970f713-4a7a-4125-892c-6a34139371d8 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_503_sample_1 + identifier: + - value: 2920ca1c-6035-4350-ada4-c60d485dbfff + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5555-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_503_sample_1_subject + identifier: + - value: TCGA-BA-5555-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8970f713-4a7a-4125-892c-6a34139371d8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_503_sample_2 + identifier: + - value: 99ca3c12-0d63-428f-8b1b-03e4a3e8e233 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-5555-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_503_sample_2_subject + identifier: + - value: TCGA-BA-5555-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8970f713-4a7a-4125-892c-6a34139371d8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_504_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_504_diagnosis_0 + identifier: + - value: 51ca5228-56c7-5d68-9285-1bbfbe8b4492 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_504 + identifier: + - value: 890b5a8b-703d-428d-8833-bc0ce26e80aa + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7370 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 26468 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_504_sample_0 + identifier: + - value: 339524bc-bc1f-403c-a12f-6e8ce72fba50 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7370-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_504_sample_0_subject + identifier: + - value: TCGA-CR-7370-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 890b5a8b-703d-428d-8833-bc0ce26e80aa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_504_sample_1 + identifier: + - value: 0e357973-d52d-4fc7-8099-7b87458745e2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7370-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_504_sample_1_subject + identifier: + - value: TCGA-CR-7370-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 890b5a8b-703d-428d-8833-bc0ce26e80aa + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_505_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_505_diagnosis_0 + identifier: + - value: 18cabf3d-233d-5ad2-a5d3-a2a10677c99a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_505 + identifier: + - value: 2855bf40-e5e1-4519-b47a-327bfc275279 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BA-A4II + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 17011 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_505_sample_0 + identifier: + - value: 81bbc439-0c8c-4d39-bef2-03901b31c50e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4II-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_505_sample_0_subject + identifier: + - value: TCGA-BA-A4II-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2855bf40-e5e1-4519-b47a-327bfc275279 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 498 + unit: + coding: *id001 + quantity_collected: + value_decimal: 190 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_505_sample_1 + identifier: + - value: a76bfc3e-fa46-4a65-88e7-c644c8b20098 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BA-A4II-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_505_sample_1_subject + identifier: + - value: TCGA-BA-A4II-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2855bf40-e5e1-4519-b47a-327bfc275279 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 574 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_506_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_506_diagnosis_0 + identifier: + - value: 066a4a47-3b4a-582d-984d-476fa8a4fc57 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_506 + identifier: + - value: 2e73e016-61ff-4f23-9ca9-fd48d9050d82 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7422 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22098 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1997-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_506_sample_0 + identifier: + - value: 63bdeeca-a7b1-47fb-9945-c24f7513c56c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7422-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_506_sample_0_subject + identifier: + - value: TCGA-CV-7422-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2e73e016-61ff-4f23-9ca9-fd48d9050d82 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_506_sample_1 + identifier: + - value: 2c2db97c-8c8d-4f1e-ab73-469238609d61 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7422-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_506_sample_1_subject + identifier: + - value: TCGA-CV-7422-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2e73e016-61ff-4f23-9ca9-fd48d9050d82 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_506_sample_2 + identifier: + - value: 9e25f49c-cd83-4171-9e07-51aca3fb1019 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7422-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_506_sample_2_subject + identifier: + - value: TCGA-CV-7422-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2e73e016-61ff-4f23-9ca9-fd48d9050d82 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_507_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_507_diagnosis_0 + identifier: + - value: 5d8267c6-4156-5145-b6e3-49c68f8cabfb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_507 + identifier: + - value: 044579ef-16a6-4f00-b951-edc423d8a14f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-5361 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 29383 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2007-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_507_sample_0 + identifier: + - value: c807171a-4433-4246-a454-c5cf768da8aa + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5361-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_507_sample_0_subject + identifier: + - value: TCGA-CN-5361-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 044579ef-16a6-4f00-b951-edc423d8a14f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_507_sample_1 + identifier: + - value: 5b2581d8-c087-4caa-b9ce-bc0168fbfefa + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5361-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_507_sample_1_subject + identifier: + - value: TCGA-CN-5361-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 044579ef-16a6-4f00-b951-edc423d8a14f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_507_sample_2 + identifier: + - value: 2877214f-4aab-46cf-b052-b6e7d2662ff5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-5361-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_507_sample_2_subject + identifier: + - value: TCGA-CN-5361-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 044579ef-16a6-4f00-b951-edc423d8a14f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_508_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_508_diagnosis_0 + identifier: + - value: 6459d972-a02b-5a11-a7ef-12f699047036 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_508 + identifier: + - value: a9017cd4-df30-46eb-b08f-39540b15243f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-5248 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19441 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2006-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_508_sample_0 + identifier: + - value: a4dca71f-e53a-4bd0-9d1b-3381ed188a41 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5248-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_508_sample_0_subject + identifier: + - value: TCGA-CR-5248-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a9017cd4-df30-46eb-b08f-39540b15243f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_508_sample_1 + identifier: + - value: 0771e98b-4e65-450d-afc2-33d4e30b3df2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-5248-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_508_sample_1_subject + identifier: + - value: TCGA-CR-5248-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a9017cd4-df30-46eb-b08f-39540b15243f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_509_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_509_diagnosis_0 + identifier: + - value: 2c09a792-df0e-513e-a9a2-7e363de6435e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_509 + identifier: + - value: fcb0c5e5-f63c-41b3-ae0e-3d1d6aaa66e4 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-F7-A623 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25592 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_509_sample_0 + identifier: + - value: 5f14a8c0-f19e-4a67-b6dc-907196ab34f6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A623-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_509_sample_0_subject + identifier: + - value: TCGA-F7-A623-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fcb0c5e5-f63c-41b3-ae0e-3d1d6aaa66e4 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 101 + unit: + coding: *id001 + quantity_collected: + value_decimal: 800 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_509_sample_1 + identifier: + - value: 33c19ae3-107a-4b64-9906-5b775025cd8f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A623-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_509_sample_1_subject + identifier: + - value: TCGA-F7-A623-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fcb0c5e5-f63c-41b3-ae0e-3d1d6aaa66e4 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 101 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_509_sample_2 + identifier: + - value: bb90f8e2-c872-4ded-9d10-5110f023762f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-F7-A623-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_509_sample_2_subject + identifier: + - value: TCGA-F7-A623-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fcb0c5e5-f63c-41b3-ae0e-3d1d6aaa66e4 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_510_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_510_diagnosis_0 + identifier: + - value: 6739697d-d536-5d38-813f-5a4973a97cb9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_510 + identifier: + - value: 5fe17dde-ef75-49a2-90f8-0647077b6ca5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-A49A + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21995 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C05.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_510_sample_0 + identifier: + - value: 77234a56-cad6-4b84-aabb-032be68f7dea + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A49A-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_510_sample_0_subject + identifier: + - value: TCGA-CN-A49A-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5fe17dde-ef75-49a2-90f8-0647077b6ca5 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 309 + unit: + coding: *id001 + quantity_collected: + value_decimal: 280 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_510_sample_1 + identifier: + - value: 8e00c51b-cc4e-4de3-ad9d-8ffe30f2ab0b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-A49A-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_510_sample_1_subject + identifier: + - value: TCGA-CN-A49A-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5fe17dde-ef75-49a2-90f8-0647077b6ca5 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 309 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_511_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_511_diagnosis_0 + identifier: + - value: b9143400-abdf-5f03-9771-ebafe5bb5d43 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_511 + identifier: + - value: f8acc36b-1e7f-44b8-83b7-f894ad201833 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7371 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 16568 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_511_sample_0 + identifier: + - value: ac9f5493-c06b-40dd-b80d-7be718d27289 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7371-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_511_sample_0_subject + identifier: + - value: TCGA-CR-7371-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f8acc36b-1e7f-44b8-83b7-f894ad201833 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_511_sample_1 + identifier: + - value: 5a5005d4-6cd9-431a-89ec-ce6d34b0fc7d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7371-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_511_sample_1_subject + identifier: + - value: TCGA-CR-7371-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f8acc36b-1e7f-44b8-83b7-f894ad201833 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_512_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_512_diagnosis_0 + identifier: + - value: a37311af-d40e-5c8f-ba14-b3b2ae22e486 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_512 + identifier: + - value: 171890ae-0391-4d8c-9bd2-090d866a2c5b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-6997 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24298 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_512_sample_0 + identifier: + - value: b4c9a3aa-151e-478b-bc18-ce793b68ae09 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6997-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_512_sample_0_subject + identifier: + - value: TCGA-CN-6997-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 171890ae-0391-4d8c-9bd2-090d866a2c5b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_512_sample_1 + identifier: + - value: 00a721c6-6cb7-4408-a63a-6dae9310a3fe + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6997-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_512_sample_1_subject + identifier: + - value: TCGA-CN-6997-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 171890ae-0391-4d8c-9bd2-090d866a2c5b + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_512_sample_2 + identifier: + - value: 8b73f661-e1ec-4bcb-9eea-a5e66237229a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-6997-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_512_sample_2_subject + identifier: + - value: TCGA-CN-6997-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 171890ae-0391-4d8c-9bd2-090d866a2c5b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_513_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_513_diagnosis_0 + identifier: + - value: b7c8a51e-1403-54ce-a94e-ca7cfc05c21b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_513 + identifier: + - value: 10f53522-9ae7-47b9-80aa-b4b481561465 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-HD-7754 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25365 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_513_sample_0 + identifier: + - value: adb496a1-07eb-45b9-8690-00184143300e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7754-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_513_sample_0_subject + identifier: + - value: TCGA-HD-7754-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10f53522-9ae7-47b9-80aa-b4b481561465 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_513_sample_1 + identifier: + - value: 3fb86c71-0f8b-4022-b19f-d394401df9fe + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7754-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_513_sample_1_subject + identifier: + - value: TCGA-HD-7754-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10f53522-9ae7-47b9-80aa-b4b481561465 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_513_sample_2 + identifier: + - value: 97d5f4b1-b8a5-4fb1-8af6-f0e6cfc302f6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7754-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_513_sample_2_subject + identifier: + - value: TCGA-HD-7754-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10f53522-9ae7-47b9-80aa-b4b481561465 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_514_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_514_diagnosis_0 + identifier: + - value: 424f3fdd-09f1-57a2-99de-10c13b9be653 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_514 + identifier: + - value: 37159b2b-e564-47a9-adaa-91b9571ef9de + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-A6EP + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22674 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, large cell, nonkeratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8072/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_514_sample_0 + identifier: + - value: 1e8ad4ff-09db-44f6-9527-b10ac22453d6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EP-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_514_sample_0_subject + identifier: + - value: TCGA-D6-A6EP-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 37159b2b-e564-47a9-adaa-91b9571ef9de + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_514_sample_1 + identifier: + - value: 661cafd9-0cf9-4c6f-b541-293bdecf3ede + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EP-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_514_sample_1_subject + identifier: + - value: TCGA-D6-A6EP-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 37159b2b-e564-47a9-adaa-91b9571ef9de + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 107 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_514_sample_2 + identifier: + - value: 434adba3-549a-45f7-b89b-76737678ae0e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-A6EP-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_514_sample_2_subject + identifier: + - value: TCGA-D6-A6EP-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 37159b2b-e564-47a9-adaa-91b9571ef9de + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 107 + unit: + coding: *id001 + quantity_collected: + value_decimal: 300 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_515_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_515_diagnosis_0 + identifier: + - value: 8f722b2d-eb3e-5b8b-8b36-429137cb0a3f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_515 + identifier: + - value: 16779eed-f386-4e8f-8475-04d33b9dd160 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7383 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 29122 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2008-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_515_sample_0 + identifier: + - value: 6237b644-9903-4f45-8b07-6c610b1342b8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7383-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_515_sample_0_subject + identifier: + - value: TCGA-CR-7383-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 16779eed-f386-4e8f-8475-04d33b9dd160 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_515_sample_1 + identifier: + - value: 887261fe-5b99-4722-aca7-4e63a0b63336 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7383-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_515_sample_1_subject + identifier: + - value: TCGA-CR-7383-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 16779eed-f386-4e8f-8475-04d33b9dd160 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_516_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_516_diagnosis_0 + identifier: + - value: b5b027c4-6ae8-4c42-9ffc-46738ec336b9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_516 + identifier: + - value: 5b6615ec-24a8-423d-9e16-cc86d6c2c2d3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-VICC-671452 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_516_sample_0 + identifier: + - value: eddc8197-6d13-4eef-bb1d-06d1b8df5395 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-VICC-671452-unk-1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_516_sample_0_subject + identifier: + - value: GENIE-VICC-671452-unk-1 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5b6615ec-24a8-423d-9e16-cc86d6c2c2d3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_517_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_517_diagnosis_0 + identifier: + - value: 0722d8c6-5481-4736-a9ea-24253edffa93 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_517 + identifier: + - value: 36034809-4abd-4668-9688-69da10154270 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005284 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_517_sample_0 + identifier: + - value: f02ce49d-85b8-4704-9dbb-8e012090fbd5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005284-2016 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_517_sample_0_subject + identifier: + - value: GENIE-DFCI-005284-2016 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 36034809-4abd-4668-9688-69da10154270 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_518_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_518_diagnosis_0 + identifier: + - value: 4dbbefaa-8e8e-4a44-943b-48687f123673 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_518 + identifier: + - value: 836b7552-c6f9-4468-81c6-2a5ccea403c5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010088 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_518_sample_0 + identifier: + - value: b5da1115-1fe3-49a4-892b-ef43e64dbee4 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010088-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_518_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010088-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 836b7552-c6f9-4468-81c6-2a5ccea403c5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_519_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_519_diagnosis_0 + identifier: + - value: 1674c3b2-c0b1-4395-9822-81016a649ad8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_519 + identifier: + - value: 9b5f15b2-a15d-45a1-949c-765c94f463da + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-4664 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_519_sample_0 + identifier: + - value: 2bd6f2fa-881f-4287-a616-d43d33a5e551 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-4664-11636 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_519_sample_0_subject + identifier: + - value: GENIE-MDA-4664-11636 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 9b5f15b2-a15d-45a1-949c-765c94f463da + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_520_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_520_diagnosis_0 + identifier: + - value: 155a3146-d68b-4058-abe2-3ae8713641ce + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_520 + identifier: + - value: 22abf2a2-f00e-49c0-ba74-1b5785ebaef3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MDA-5361 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_520_sample_0 + identifier: + - value: a7b07575-200a-4a32-8faa-075ded8667cc + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MDA-5361-16435 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_520_sample_0_subject + identifier: + - value: GENIE-MDA-5361-16435 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 22abf2a2-f00e-49c0-ba74-1b5785ebaef3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_521_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_521_diagnosis_0 + identifier: + - value: f068b7ad-5b43-44f0-95b3-33ead995b8cb + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_521 + identifier: + - value: 2cee5430-02b8-4ba9-b81c-67ea32b9f61a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0010161 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_521_sample_0 + identifier: + - value: ea42167d-71c9-4eda-8153-2b207208d97d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0010161-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_521_sample_0_subject + identifier: + - value: GENIE-MSK-P-0010161-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 2cee5430-02b8-4ba9-b81c-67ea32b9f61a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_522_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_522_diagnosis_0 + identifier: + - value: 99aa5d5b-c650-47f5-b485-da3d78661529 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_522 + identifier: + - value: 3ac8ecbf-2ea3-48b9-b820-ff15ef89795b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0018925 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_522_sample_0 + identifier: + - value: 5007e321-c75c-45c2-b4a7-0d3cbde5280a + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0018925-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_522_sample_0_subject + identifier: + - value: GENIE-MSK-P-0018925-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3ac8ecbf-2ea3-48b9-b820-ff15ef89795b + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_523_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_523_diagnosis_0 + identifier: + - value: f1143020-2e95-4028-a2bf-c03a5ba6ea4e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_523 + identifier: + - value: a20c5ca1-e458-46d2-af06-582f4f2001e5 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD14041 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18006 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_523_sample_0 + identifier: + - value: fe72277e-ae77-486d-b5a9-844c483267eb + system: http://crdc.nci.nih.gov/gdc + - value: AD14041_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_523_sample_0_subject + identifier: + - value: AD14041_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a20c5ca1-e458-46d2-af06-582f4f2001e5 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_524_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_524_diagnosis_0 + identifier: + - value: 826319f7-67b5-481a-998b-781e3ded01c1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_524 + identifier: + - value: 8e1d6997-e598-41f2-9982-62eefd8bd409 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-GRCC-22f8acca + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_524_sample_0 + identifier: + - value: 7aa50a3f-dd6c-496c-89e2-2d8d6d136acf + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-GRCC-22f8acca-sample-a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_524_sample_0_subject + identifier: + - value: GENIE-GRCC-22f8acca-sample-a + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 8e1d6997-e598-41f2-9982-62eefd8bd409 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_525_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_525_diagnosis_0 + identifier: + - value: 0f72e73b-f462-4eef-9d1e-95e83c1f2aaf + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_525 + identifier: + - value: a9b101be-b7a0-41b3-8cef-7d4205263980 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD5362 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 16283 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_525_sample_0 + identifier: + - value: 9f4929bc-09a7-47b8-9720-d6f829b51a13 + system: http://crdc.nci.nih.gov/gdc + - value: AD5362_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_525_sample_0_subject + identifier: + - value: AD5362_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: a9b101be-b7a0-41b3-8cef-7d4205263980 + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_526_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_526_diagnosis_0 + identifier: + - value: da37f4a4-3f09-4771-a1a0-9b2ce6e0df03 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_526 + identifier: + - value: f728ce62-2f84-4fda-92fa-7a8b8132751d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: AD2161 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22054 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Carcinoma, undifferentiated, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8020/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_526_sample_0 + identifier: + - value: 7f5f0ba4-3eb5-462a-8db8-31faca9d0d27 + system: http://crdc.nci.nih.gov/gdc + - value: AD2161_sample + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_526_sample_0_subject + identifier: + - value: AD2161_sample + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f728ce62-2f84-4fda-92fa-7a8b8132751d + system: http://crdc.nci.nih.gov/gdc#case_id + tumor_status_at_collection: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_527_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_527_diagnosis_0 + identifier: + - value: 1b2f7aa9-bc17-4cfa-8d93-b5a7bdd68bfe + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_527 + identifier: + - value: 7a11ded5-859b-498c-8ebe-5edad3b9c292 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0015451 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_527_sample_0 + identifier: + - value: 8a18a085-a8a0-4fd0-9468-33e10fe1c55d + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0015451-T01-IM6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_527_sample_0_subject + identifier: + - value: GENIE-MSK-P-0015451-T01-IM6 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7a11ded5-859b-498c-8ebe-5edad3b9c292 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_528_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_528_diagnosis_0 + identifier: + - value: d1841d22-3350-4037-918a-bb399ed85963 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_528 + identifier: + - value: 1bd8c4bb-99b5-4d55-bbbc-0feaeda12dc1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-005202 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_528_sample_0 + identifier: + - value: 97064320-d382-4d87-a302-72490d7577d6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-005202-1165 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_528_sample_0_subject + identifier: + - value: GENIE-DFCI-005202-1165 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 1bd8c4bb-99b5-4d55-bbbc-0feaeda12dc1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_529_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_529_diagnosis_0 + identifier: + - value: 274578bf-55cd-4807-9c8e-573db026da1d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_529 + identifier: + - value: 10a1247b-685b-4db2-9829-97914280f607 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0002592 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_529_sample_0 + identifier: + - value: a75ac689-6228-4806-b699-874f8ec28ae1 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0002592-T01-IM3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_529_sample_0_subject + identifier: + - value: GENIE-MSK-P-0002592-T01-IM3 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 10a1247b-685b-4db2-9829-97914280f607 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_530_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_530_diagnosis_0 + identifier: + - value: a433a5fa-fd34-4ab5-a117-29614a2c7f9a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_530 + identifier: + - value: 969fd0e5-3e20-499f-ba4e-e2312de3a93e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0013513 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_530_sample_0 + identifier: + - value: f2ec974c-b952-4450-947b-11c39bbaf248 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0013513-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_530_sample_0_subject + identifier: + - value: GENIE-MSK-P-0013513-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 969fd0e5-3e20-499f-ba4e-e2312de3a93e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_531_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_531_diagnosis_0 + identifier: + - value: 1ad86ae6-e1df-4578-9639-e768e6711e61 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_531 + identifier: + - value: f85458b4-167d-4fd0-be8e-0f9e85095bf0 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0008033 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_531_sample_0 + identifier: + - value: 28cb9e1d-c34b-4909-a387-5a5c60bcd6e3 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0008033-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_531_sample_0_subject + identifier: + - value: GENIE-MSK-P-0008033-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f85458b4-167d-4fd0-be8e-0f9e85095bf0 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_532_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_532_diagnosis_0 + identifier: + - value: 99aab93f-633d-4ce6-8ccf-36cb05c5d2cc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_532 + identifier: + - value: 23f54bf4-cb23-46c8-a9fb-30fbdfa84012 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-MSK-P-0007575 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8010/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_532_sample_0 + identifier: + - value: b1d7b582-2302-44fb-a98f-13372ca17247 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-MSK-P-0007575-T01-IM5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Metastatic + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_532_sample_0_subject + identifier: + - value: GENIE-MSK-P-0007575-T01-IM5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 23f54bf4-cb23-46c8-a9fb-30fbdfa84012 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_533_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_533_diagnosis_0 + identifier: + - value: 9076e2ad-9cef-4efc-99d7-387d250445ee + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_533 + identifier: + - value: 24a42ec3-ae85-446a-a5d8-410bd98dece1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-025889 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_533_sample_0 + identifier: + - value: 678dfc0e-f085-4c85-b444-8fc1604bdcfe + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-025889-116451 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_533_sample_0_subject + identifier: + - value: GENIE-DFCI-025889-116451 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 24a42ec3-ae85-446a-a5d8-410bd98dece1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_534_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_534_diagnosis_0 + identifier: + - value: 09912911-2865-490c-aaca-89f4cc1bee36 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_534 + identifier: + - value: d3db3810-26bd-4953-95fa-6493e9f4f6d3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008390 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_534_sample_0 + identifier: + - value: 7894955b-ac0e-46ee-a5b3-c023cd1e87b6 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008390-5815 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_534_sample_0_subject + identifier: + - value: GENIE-DFCI-008390-5815 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: d3db3810-26bd-4953-95fa-6493e9f4f6d3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_535_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_535_diagnosis_0 + identifier: + - value: 5b91d8ab-6ed3-4c0a-a56b-8f0e151eaf5a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_535 + identifier: + - value: c7e547f7-5a1f-49d4-bc51-aa56d4d2703e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-000195 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_535_sample_0 + identifier: + - value: 52beca45-8506-41fa-b0a0-3a8c24c9d7fe + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-000195-4559 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_535_sample_0_subject + identifier: + - value: GENIE-DFCI-000195-4559 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: c7e547f7-5a1f-49d4-bc51-aa56d4d2703e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_536_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_536_diagnosis_0 + identifier: + - value: 4943c82a-30d2-4c85-a233-032a49ca801d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_536 + identifier: + - value: 31eee15c-f55f-480d-aa60-3b48bbc5bb0c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-008342 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_536_sample_0 + identifier: + - value: e01da120-9c9d-4ef7-8568-525f74222dd5 + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-008342-5809 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_536_sample_0_subject + identifier: + - value: GENIE-DFCI-008342-5809 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 31eee15c-f55f-480d-aa60-3b48bbc5bb0c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_537_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_537_diagnosis_0 + identifier: + - value: 2dd60fd1-68e1-519b-af66-00c32d0cb6d4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_537 + identifier: + - value: 3d2ff6c0-8c03-440d-8ec1-231862bd6713 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A8ZB + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25192 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_537_sample_0 + identifier: + - value: 44c64654-0e37-4c13-b4fa-aaf9c6644445 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8ZB-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_537_sample_0_subject + identifier: + - value: TCGA-QK-A8ZB-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3d2ff6c0-8c03-440d-8ec1-231862bd6713 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_537_sample_1 + identifier: + - value: 936a8a93-6559-4bf8-9c51-e81ec4f2aff7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8ZB-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_537_sample_1_subject + identifier: + - value: TCGA-QK-A8ZB-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3d2ff6c0-8c03-440d-8ec1-231862bd6713 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 30 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_537_sample_2 + identifier: + - value: 17a0a479-3b48-4852-ab06-dd33d6f7788a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A8ZB-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_537_sample_2_subject + identifier: + - value: TCGA-QK-A8ZB-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3d2ff6c0-8c03-440d-8ec1-231862bd6713 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 30 + unit: + coding: *id001 + quantity_collected: + value_decimal: 200 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_538_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_538_diagnosis_0 + identifier: + - value: d670dce6-9fa8-402a-8b79-081ec26ebe25 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_538 + identifier: + - value: cb4ba52f-606a-4d8e-8ee4-5c76a803d42e + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-000843 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_538_sample_0 + identifier: + - value: 85fa5941-b6df-4eea-97e1-a7b4ae310bdb + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-000843-6962 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_538_sample_0_subject + identifier: + - value: GENIE-DFCI-000843-6962 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: cb4ba52f-606a-4d8e-8ee4-5c76a803d42e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_539_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_539_diagnosis_0 + identifier: + - value: cf19d9da-2868-599e-9281-91b9e064078d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_539 + identifier: + - value: fc3ea52b-67ac-4876-949d-5464c436f3db + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CR-7374 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24558 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_539_sample_0 + identifier: + - value: ece42fcc-b771-42af-92c4-39fd74b645c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7374-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_539_sample_0_subject + identifier: + - value: TCGA-CR-7374-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fc3ea52b-67ac-4876-949d-5464c436f3db + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_539_sample_1 + identifier: + - value: 77be0d91-0525-439f-bb34-3a0702c81085 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CR-7374-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_539_sample_1_subject + identifier: + - value: TCGA-CR-7374-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: fc3ea52b-67ac-4876-949d-5464c436f3db + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_540_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_540_diagnosis_0 + identifier: + - value: f73d9c17-c497-5025-84d8-e9adaf48a245 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_540 + identifier: + - value: 7bfef2dd-5f82-4521-9369-0329e41faf1b + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-MT-A67G + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19394 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_540_sample_0 + identifier: + - value: 6b690841-3ad9-4919-8913-8f291ee95868 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MT-A67G-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_540_sample_0_subject + identifier: + - value: TCGA-MT-A67G-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7bfef2dd-5f82-4521-9369-0329e41faf1b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 85 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_540_sample_1 + identifier: + - value: 25588932-d586-4a17-b18e-4ede4292ce9e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MT-A67G-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_540_sample_1_subject + identifier: + - value: TCGA-MT-A67G-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7bfef2dd-5f82-4521-9369-0329e41faf1b + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_540_sample_2 + identifier: + - value: 7206e2ea-ad1d-45d4-ba3c-fc1f39fc52ea + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-MT-A67G-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_540_sample_2_subject + identifier: + - value: TCGA-MT-A67G-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 7bfef2dd-5f82-4521-9369-0329e41faf1b + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 85 + unit: + coding: *id001 + quantity_collected: + value_decimal: 110 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_541_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_541_diagnosis_0 + identifier: + - value: 2edff908-b791-5c44-b0ed-cdbad3c1a249 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_541 + identifier: + - value: 20ad4ac0-6a87-461f-83a5-fded51bf821a + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7418 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22805 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1996-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_541_sample_0 + identifier: + - value: 2e5b2590-4227-4265-a837-8175920e4d01 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7418-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_541_sample_0_subject + identifier: + - value: TCGA-CV-7418-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 20ad4ac0-6a87-461f-83a5-fded51bf821a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_541_sample_1 + identifier: + - value: 26eac019-6e9b-4ab1-aa1b-323f76d9aef3 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7418-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_541_sample_1_subject + identifier: + - value: TCGA-CV-7418-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 20ad4ac0-6a87-461f-83a5-fded51bf821a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_541_sample_2 + identifier: + - value: ccd7a7be-3065-4f30-8d21-94bfdc0b4703 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7418-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_541_sample_2_subject + identifier: + - value: TCGA-CV-7418-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 20ad4ac0-6a87-461f-83a5-fded51bf821a + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_541_sample_3 + identifier: + - value: cc37f4d1-d8ae-4367-8abf-7c6da579d09e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7418-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_541_sample_3_subject + identifier: + - value: TCGA-CV-7418-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 20ad4ac0-6a87-461f-83a5-fded51bf821a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_542_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_542_diagnosis_0 + identifier: + - value: 98a4badd-be86-5ac9-b0d9-9099d5bdcdef + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_542 + identifier: + - value: 5e25ab76-a8ab-4779-aa03-8de658f18da1 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7247 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20433 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1995-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_542_sample_0 + identifier: + - value: 13da732f-058d-4635-a2f0-81e73c725b8d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7247-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_542_sample_0_subject + identifier: + - value: TCGA-CV-7247-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5e25ab76-a8ab-4779-aa03-8de658f18da1 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_542_sample_1 + identifier: + - value: f84ae44b-4bb7-4841-aee0-139cd79b9680 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7247-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_542_sample_1_subject + identifier: + - value: TCGA-CV-7247-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5e25ab76-a8ab-4779-aa03-8de658f18da1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_542_sample_2 + identifier: + - value: 2e9cdad5-53ec-4b5e-8a1e-4f8abee04149 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7247-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_542_sample_2_subject + identifier: + - value: TCGA-CV-7247-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5e25ab76-a8ab-4779-aa03-8de658f18da1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_542_sample_3 + identifier: + - value: 5ec51826-98c1-49d2-a990-7a95ee636753 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7247-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_542_sample_3_subject + identifier: + - value: TCGA-CV-7247-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5e25ab76-a8ab-4779-aa03-8de658f18da1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_543_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_543_diagnosis_0 + identifier: + - value: e61558f0-d90a-5bd0-8485-ba159dba3010 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_543 + identifier: + - value: f68237e7-7fc0-4b6b-8095-b49515ddd169 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-7862 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 24823 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_543_sample_0 + identifier: + - value: 091478b2-f8c5-4ad8-9c89-06a48728fa2d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7862-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_543_sample_0_subject + identifier: + - value: TCGA-BB-7862-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f68237e7-7fc0-4b6b-8095-b49515ddd169 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_543_sample_1 + identifier: + - value: a61be572-405b-4b16-b554-7fa6c12a48a4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7862-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_543_sample_1_subject + identifier: + - value: TCGA-BB-7862-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f68237e7-7fc0-4b6b-8095-b49515ddd169 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_543_sample_2 + identifier: + - value: fbf59d12-7047-49b1-9002-00030c797438 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-7862-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_543_sample_2_subject + identifier: + - value: TCGA-BB-7862-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: f68237e7-7fc0-4b6b-8095-b49515ddd169 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_544_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_544_diagnosis_0 + identifier: + - value: d9cc35a1-8103-5f6b-8d97-cc64c564c677 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_544 + identifier: + - value: 0abe0b8f-fd93-43e8-b78f-48a7c3f96868 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A7JH + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21558 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_544_sample_0 + identifier: + - value: 980726e2-9e0c-4212-b5aa-69e139fc3be7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JH-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_544_sample_0_subject + identifier: + - value: TCGA-UF-A7JH-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0abe0b8f-fd93-43e8-b78f-48a7c3f96868 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 385 + unit: + coding: *id001 + quantity_collected: + value_decimal: 120 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_544_sample_1 + identifier: + - value: 1c9d867a-6fba-49a1-99ba-63bd01942397 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JH-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_544_sample_1_subject + identifier: + - value: TCGA-UF-A7JH-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0abe0b8f-fd93-43e8-b78f-48a7c3f96868 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_544_sample_2 + identifier: + - value: 2b803b39-f13c-4335-9845-05bb61830015 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JH-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_544_sample_2_subject + identifier: + - value: TCGA-UF-A7JH-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0abe0b8f-fd93-43e8-b78f-48a7c3f96868 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 385 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_545_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_545_diagnosis_0 + identifier: + - value: 24e37f06-2587-52ee-bcb3-40688978538e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_545 + identifier: + - value: 03c3ae62-d0aa-412e-bd3c-4577fc9f919c + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-A6UM + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19194 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_545_sample_0 + identifier: + - value: c4aabbde-a46a-403e-b974-7b61b964a1b8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-A6UM-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_545_sample_0_subject + identifier: + - value: TCGA-BB-A6UM-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 03c3ae62-d0aa-412e-bd3c-4577fc9f919c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1149 + unit: + coding: *id001 + quantity_collected: + value_decimal: 110 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_545_sample_1 + identifier: + - value: 99404948-9837-40eb-bf38-c1cfe1b9a88c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-A6UM-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_545_sample_1_subject + identifier: + - value: TCGA-BB-A6UM-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 03c3ae62-d0aa-412e-bd3c-4577fc9f919c + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_545_sample_2 + identifier: + - value: ccc0e6ba-cf8b-45e4-9f0b-dd2422b3e470 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-A6UM-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_545_sample_2_subject + identifier: + - value: TCGA-BB-A6UM-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 03c3ae62-d0aa-412e-bd3c-4577fc9f919c + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1149 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_546_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_546_diagnosis_0 + identifier: + - value: 35c83c03-b2ab-5f6b-a231-66a3f879a217 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_546 + identifier: + - value: 3a867df4-d548-4408-a90b-441ded53b7b6 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A5Q5 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19728 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2004-01-01' + condition: + coding: + - code: Basaloid squamous cell carcinoma + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C09.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8083/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_546_sample_0 + identifier: + - value: 3f5cd265-0dd3-40c3-94b8-e92d18ce87b0 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5Q5-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_546_sample_0_subject + identifier: + - value: TCGA-P3-A5Q5-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3a867df4-d548-4408-a90b-441ded53b7b6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 3207 + unit: + coding: *id001 + quantity_collected: + value_decimal: 30 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_546_sample_1 + identifier: + - value: 2e1b4cf3-61fe-452c-b800-f9bc53333713 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5Q5-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_546_sample_1_subject + identifier: + - value: TCGA-P3-A5Q5-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3a867df4-d548-4408-a90b-441ded53b7b6 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 3207 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_546_sample_2 + identifier: + - value: 3b3502ab-ab9f-49d7-be08-243a7022463f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5Q5-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_546_sample_2_subject + identifier: + - value: TCGA-P3-A5Q5-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 3a867df4-d548-4408-a90b-441ded53b7b6 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_547_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_547_diagnosis_0 + identifier: + - value: 86e71958-485e-53c6-831a-c456ec617b7b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_547 + identifier: + - value: 5c48e21f-1fe9-4007-9b0c-7ca766586fff + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-HD-7229 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 22076 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2011-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_547_sample_0 + identifier: + - value: 1169973a-8575-4d2b-8da8-36a83aa5f947 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7229-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_547_sample_0_subject + identifier: + - value: TCGA-HD-7229-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5c48e21f-1fe9-4007-9b0c-7ca766586fff + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_547_sample_1 + identifier: + - value: f1367475-a5f1-4a0f-aa73-5a703a3accaf + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7229-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_547_sample_1_subject + identifier: + - value: TCGA-HD-7229-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5c48e21f-1fe9-4007-9b0c-7ca766586fff + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_547_sample_2 + identifier: + - value: 9fbf3123-c654-4f2c-b41a-ac4dc029a5d9 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-HD-7229-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_547_sample_2_subject + identifier: + - value: TCGA-HD-7229-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5c48e21f-1fe9-4007-9b0c-7ca766586fff + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_548_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_548_diagnosis_0 + identifier: + - value: 6284d2ec-e8b6-5cce-957d-f55704379de9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_548 + identifier: + - value: b3dbf9ad-9602-4e44-beac-1cfa5f8bba5d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-TN-A7HJ + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18809 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_548_sample_0 + identifier: + - value: 50df1144-990e-4357-8a15-132289bce0d8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HJ-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_548_sample_0_subject + identifier: + - value: TCGA-TN-A7HJ-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b3dbf9ad-9602-4e44-beac-1cfa5f8bba5d + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_548_sample_1 + identifier: + - value: 412fe306-9755-4efe-abb0-9af695b5691e + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HJ-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_548_sample_1_subject + identifier: + - value: TCGA-TN-A7HJ-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b3dbf9ad-9602-4e44-beac-1cfa5f8bba5d + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 45 + unit: + coding: *id001 + quantity_collected: + value_decimal: 160 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_548_sample_2 + identifier: + - value: cdc66ca4-8864-4f22-bc4e-8fb5e073937f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HJ-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_548_sample_2_subject + identifier: + - value: TCGA-TN-A7HJ-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: b3dbf9ad-9602-4e44-beac-1cfa5f8bba5d + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 45 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_549_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_549_diagnosis_0 + identifier: + - value: 26ffab97-fa9a-5135-b283-8c4aebe51a26 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_549 + identifier: + - value: 0858c8b7-e2eb-4461-b65e-9d476029ad8d + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7250 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23489 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2000-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_549_sample_0 + identifier: + - value: 3e6bc216-301a-4f24-911c-8c3610e4a015 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7250-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_549_sample_0_subject + identifier: + - value: TCGA-CV-7250-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0858c8b7-e2eb-4461-b65e-9d476029ad8d + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_549_sample_1 + identifier: + - value: 6f55766a-d980-414a-be4a-369e93ec3436 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7250-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_549_sample_1_subject + identifier: + - value: TCGA-CV-7250-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0858c8b7-e2eb-4461-b65e-9d476029ad8d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_549_sample_2 + identifier: + - value: b4f8ddc9-0ab4-447e-8292-5dcf8a9085ee + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7250-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_549_sample_2_subject + identifier: + - value: TCGA-CV-7250-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0858c8b7-e2eb-4461-b65e-9d476029ad8d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_549_sample_3 + identifier: + - value: f5472b70-32c8-48b0-9051-f9b33272ffd6 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7250-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_549_sample_3_subject + identifier: + - value: TCGA-CV-7250-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0858c8b7-e2eb-4461-b65e-9d476029ad8d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_550_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_550_diagnosis_0 + identifier: + - value: cecde3bd-c011-5cd9-8071-912a0f342eb8 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_550 + identifier: + - value: 68f612b7-33b4-4ca4-b012-439bfd598888 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-UF-A7JJ + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25201 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, keratinizing, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8071/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_550_sample_0 + identifier: + - value: de8517e0-d7ad-41a2-9468-bdf0106c905c + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JJ-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_550_sample_0_subject + identifier: + - value: TCGA-UF-A7JJ-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 68f612b7-33b4-4ca4-b012-439bfd598888 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 87 + unit: + coding: *id001 + quantity_collected: + value_decimal: 200 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_550_sample_1 + identifier: + - value: 392cbac9-ed5a-4f0c-9270-f45278476c73 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JJ-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_550_sample_1_subject + identifier: + - value: TCGA-UF-A7JJ-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 68f612b7-33b4-4ca4-b012-439bfd598888 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_550_sample_2 + identifier: + - value: 408c2c68-2f92-421e-b797-ecada0bfedc7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-UF-A7JJ-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_550_sample_2_subject + identifier: + - value: TCGA-UF-A7JJ-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 68f612b7-33b4-4ca4-b012-439bfd598888 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 87 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_551_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_551_diagnosis_0 + identifier: + - value: 28979d39-3da1-556a-9b82-2a9953b57989 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_551 + identifier: + - value: 4587ae9f-71fb-4582-82ff-fb407fee6445 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-P3-A5QF + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 18035 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C03.0 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_551_sample_0 + identifier: + - value: 903ed81a-057c-41ad-93de-aaa9d9c082c5 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5QF-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_551_sample_0_subject + identifier: + - value: TCGA-P3-A5QF-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4587ae9f-71fb-4582-82ff-fb407fee6445 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1200 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_551_sample_1 + identifier: + - value: d30d7d4c-0acf-4b61-9d7e-2c15e20d73a8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5QF-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_551_sample_1_subject + identifier: + - value: TCGA-P3-A5QF-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4587ae9f-71fb-4582-82ff-fb407fee6445 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 1200 + unit: + coding: *id001 + quantity_collected: + value_decimal: 20 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_551_sample_2 + identifier: + - value: 2e51af26-4d06-4b66-be71-0bebed2e4557 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-P3-A5QF-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_551_sample_2_subject + identifier: + - value: TCGA-P3-A5QF-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4587ae9f-71fb-4582-82ff-fb407fee6445 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_552_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_552_diagnosis_0 + identifier: + - value: 4e06969c-5592-59ad-b006-09cb82ce6cc9 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_552 + identifier: + - value: ebe99910-e9f2-43dc-ad57-ac2f610b60c8 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-D6-6517 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21791 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2010-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_552_sample_0 + identifier: + - value: a2dd87a8-e0d1-47c1-a8d1-70b9730aa4ba + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6517-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_552_sample_0_subject + identifier: + - value: TCGA-D6-6517-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ebe99910-e9f2-43dc-ad57-ac2f610b60c8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_552_sample_1 + identifier: + - value: 53450297-c715-4c54-ad7e-3152a1e16c45 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6517-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_552_sample_1_subject + identifier: + - value: TCGA-D6-6517-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ebe99910-e9f2-43dc-ad57-ac2f610b60c8 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_552_sample_2 + identifier: + - value: 8c099f45-3fd6-4966-8cdb-ca4b9288b1a2 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-D6-6517-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_552_sample_2_subject + identifier: + - value: TCGA-D6-6517-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: ebe99910-e9f2-43dc-ad57-ac2f610b60c8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_553_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_553_diagnosis_0 + identifier: + - value: f4e541cc-a71e-55b3-ad08-3eeb8d00f2b0 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_553 + identifier: + - value: 5ed1b22d-99ca-4c21-b5d4-851e4a6217e9 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-KU-A66S + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 25454 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Basaloid squamous cell carcinoma + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8083/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_553_sample_0 + identifier: + - value: 4bed3ece-2350-4c99-bec9-3d652fbe8c9b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A66S-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_553_sample_0_subject + identifier: + - value: TCGA-KU-A66S-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ed1b22d-99ca-4c21-b5d4-851e4a6217e9 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 150 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_553_sample_1 + identifier: + - value: 3c09f5ba-a4af-4384-948a-d6e943613f7a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A66S-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_553_sample_1_subject + identifier: + - value: TCGA-KU-A66S-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ed1b22d-99ca-4c21-b5d4-851e4a6217e9 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_553_sample_2 + identifier: + - value: a590a632-55b4-4be6-b2d8-6c8afbbe99ac + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-KU-A66S-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_553_sample_2_subject + identifier: + - value: TCGA-KU-A66S-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 5ed1b22d-99ca-4c21-b5d4-851e4a6217e9 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 150 + unit: + coding: *id001 + quantity_collected: + value_decimal: 600 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_554_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_554_diagnosis_0 + identifier: + - value: a8a92864-8cd0-5e1b-8451-ca6f3e84a857 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_554 + identifier: + - value: dcb27e14-14ef-42b2-b9a6-7e26c5afa869 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-QK-A6V9 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20461 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C10.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_554_sample_0 + identifier: + - value: 462748e0-b611-44d3-b3fd-efb762ba317b + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6V9-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_554_sample_0_subject + identifier: + - value: TCGA-QK-A6V9-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dcb27e14-14ef-42b2-b9a6-7e26c5afa869 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_554_sample_1 + identifier: + - value: 9b60705b-95c4-4079-a907-e4a4b65a3cf4 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6V9-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_554_sample_1_subject + identifier: + - value: TCGA-QK-A6V9-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dcb27e14-14ef-42b2-b9a6-7e26c5afa869 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 478 + unit: + coding: *id001 + quantity_collected: + value_decimal: 30 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_554_sample_2 + identifier: + - value: 30ad1a00-b48a-47bb-8cfa-d65e4c4ba125 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-QK-A6V9-10B + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_554_sample_2_subject + identifier: + - value: TCGA-QK-A6V9-10B + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: dcb27e14-14ef-42b2-b9a6-7e26c5afa869 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 478 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_555_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_555_diagnosis_0 + identifier: + - value: b725e6d2-92c0-5585-9de7-14bb623b472e + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_555 + identifier: + - value: 97640ef0-0259-4244-95ba-48d28c60b372 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CN-4738 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 19621 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2009-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 6th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_555_sample_0 + identifier: + - value: 8277e744-0508-47d5-9cea-11dcf7f56d35 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4738-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_555_sample_0_subject + identifier: + - value: TCGA-CN-4738-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 97640ef0-0259-4244-95ba-48d28c60b372 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_555_sample_1 + identifier: + - value: 51622170-a903-43cb-bc38-4d40c7ea170f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4738-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_555_sample_1_subject + identifier: + - value: TCGA-CN-4738-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 97640ef0-0259-4244-95ba-48d28c60b372 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_555_sample_2 + identifier: + - value: fb06ae75-8516-4cdc-ba9e-093444907fc7 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CN-4738-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_555_sample_2_subject + identifier: + - value: TCGA-CN-4738-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 97640ef0-0259-4244-95ba-48d28c60b372 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_556_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_556_diagnosis_0 + identifier: + - value: 842d6984-7c03-4ab6-95db-42fa2ea699db + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_556 + identifier: + - value: 422a72e7-fe76-411d-b59e-1f0f0812c3cf + system: http://crdc.nci.nih.gov/gdc#case_id + - value: GENIE-DFCI-010671 + system: http://crdc.nci.nih.gov/gdc#submitter_id + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_556_sample_0 + identifier: + - value: 6f9eeaa3-8bd1-479c-a0fc-98317eb458dc + system: http://crdc.nci.nih.gov/gdc + - value: GENIE-DFCI-010671-11105 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_556_sample_0_subject + identifier: + - value: GENIE-DFCI-010671-11105 + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 422a72e7-fe76-411d-b59e-1f0f0812c3cf + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_557_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_557_diagnosis_0 + identifier: + - value: 95d85e5a-b82c-59f8-b7ad-710e019cdebc + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_557 + identifier: + - value: 4b50aea4-4ad1-4bf6-9cf1-984c28a99c84 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-TN-A7HL + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 21731 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2013-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_557_sample_0 + identifier: + - value: 4a0d79fe-9eb9-456c-b483-ccf956597a3d + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HL-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_557_sample_0_subject + identifier: + - value: TCGA-TN-A7HL-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b50aea4-4ad1-4bf6-9cf1-984c28a99c84 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_557_sample_1 + identifier: + - value: 9c02fd4a-a29a-4a44-ba96-5acb6ff11f7f + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HL-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_557_sample_1_subject + identifier: + - value: TCGA-TN-A7HL-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b50aea4-4ad1-4bf6-9cf1-984c28a99c84 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 45 + unit: + coding: *id001 + quantity_collected: + value_decimal: 230 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_557_sample_2 + identifier: + - value: 1077bf93-cf23-41db-925c-c633921894cc + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-TN-A7HL-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_557_sample_2_subject + identifier: + - value: TCGA-TN-A7HL-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 4b50aea4-4ad1-4bf6-9cf1-984c28a99c84 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 45 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_558_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_558_diagnosis_0 + identifier: + - value: 7a67eecc-6f46-5181-8b64-c022d0fd0060 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_558 + identifier: + - value: 0394060d-010e-405f-983d-db525f01f2c3 + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-BB-A5HY + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 23640 + unit: + coding: &id001 + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '2012-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C13.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_558_sample_0 + identifier: + - value: 4467ee1a-7188-49d6-a0d1-c8e395e6cabb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-A5HY-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_558_sample_0_subject + identifier: + - value: TCGA-BB-A5HY-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0394060d-010e-405f-983d-db525f01f2c3 + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_558_sample_1 + identifier: + - value: 5c2b4403-cdd4-4550-ba01-d8ebad9fcbc8 + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-A5HY-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_558_sample_1_subject + identifier: + - value: TCGA-BB-A5HY-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0394060d-010e-405f-983d-db525f01f2c3 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 141 + unit: + coding: *id001 + quantity_collected: + value_decimal: 60 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_558_sample_2 + identifier: + - value: 589cdde1-ecd5-4a7b-9cbc-3186916822ab + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-BB-A5HY-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_558_sample_2_subject + identifier: + - value: TCGA-BB-A5HY-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: 0394060d-010e-405f-983d-db525f01f2c3 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + date_ended: + index_time_point: + event_type: + - coding: + - code: C142714 + system: http://ncithesaurus.nci.nih.gov + label: Study Start + tag: + - harmonized + offset_from_index: + value_decimal: 141 + unit: + coding: *id001 + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc +--- +gdc_head_and_mouth_case_559_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: gdc_head_and_mouth_example:case_559_diagnosis_0 + identifier: + - value: d20b4711-8757-5d39-a8cc-b8ece86592cd + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: gdc_head_and_mouth_example:case_559 + identifier: + - value: df132eb8-174b-4427-a16b-953e0f28bf2f + system: http://crdc.nci.nih.gov/gdc#case_id + - value: TCGA-CV-7430 + system: http://crdc.nci.nih.gov/gdc#submitter_id + age_at_diagnosis: + value_decimal: 20763 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + diagnosis_date: + date_time: '1996-01-01' + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + - code: C32.9 + system: http://hl7.org/fhir/ValueSet/icd-10 + tag: + - original + stage: + - method_type: + - coding: + - code: 7th + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: gdc_head_and_mouth_example:case_559_sample_0 + identifier: + - value: 0e0af838-3a62-44a6-9e8e-0f9ba07730fa + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7430-01A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_559_sample_0_subject + identifier: + - value: TCGA-CV-7430-01A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: df132eb8-174b-4427-a16b-953e0f28bf2f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_559_sample_1 + identifier: + - value: c22e9fe0-a052-4c6f-9fb2-e58289277e2a + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7430-11A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_559_sample_1_subject + identifier: + - value: TCGA-CV-7430-11A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: df132eb8-174b-4427-a16b-953e0f28bf2f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_559_sample_2 + identifier: + - value: 6bd53676-487f-4661-8e01-739b3b856cee + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7430-10A + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Blood Derived Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_559_sample_2_subject + identifier: + - value: TCGA-CV-7430-10A + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: df132eb8-174b-4427-a16b-953e0f28bf2f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + - id: gdc_head_and_mouth_example:case_559_sample_3 + identifier: + - value: da9132d5-4a55-4d7a-bb7f-7990af380dcb + system: http://crdc.nci.nih.gov/gdc + - value: TCGA-CV-7430-01Z + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: gdc_head_and_mouth_example:case_559_sample_3_subject + identifier: + - value: TCGA-CV-7430-01Z + system: http://crdc.nci.nih.gov/gdc#submitter_id + - value: df132eb8-174b-4427-a16b-953e0f28bf2f + system: http://crdc.nci.nih.gov/gdc#case_id + processing_activity: + - activity_type: + coding: + - code: FFPE + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc diff --git a/ccdh-pilot/imported-node-data/pdc-head-and-mouth.yaml b/ccdh-pilot/imported-node-data/pdc-head-and-mouth.yaml new file mode 100644 index 0000000..716bd2d --- /dev/null +++ b/ccdh-pilot/imported-node-data/pdc-head-and-mouth.yaml @@ -0,0 +1,12438 @@ +pdc_head_and_mouth_example_0_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_0_diagnosis_0 + identifier: + - value: 90972454-6af2-4704-bb16-c0010829f703 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_0 + identifier: + - value: 0232701d-6d00-440c-af6c-5899fbbf4142 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_0_sample_0 + identifier: + - value: d58e2a88-8b0c-4cc4-bb1a-e7734ad58209 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_0_sample_0_subject + identifier: + - value: 0232701d-6d00-440c-af6c-5899fbbf4142 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_0_sample_1 + identifier: + - value: e65dfd5a-86d6-4f54-bc0d-bd60c86a7d9b + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_0_sample_1_subject + identifier: + - value: 0232701d-6d00-440c-af6c-5899fbbf4142 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_1_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_1_diagnosis_0 + identifier: + - value: ae7a3f6c-173c-44d3-8a3e-381347861151 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_1 + identifier: + - value: 0e943de7-c277-48f2-8fa9-b2e836b03c2c + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_1_sample_0 + identifier: + - value: b6ecae8d-08a9-44e3-ac70-51331be42e55 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_1_sample_0_subject + identifier: + - value: 0e943de7-c277-48f2-8fa9-b2e836b03c2c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_1_sample_1 + identifier: + - value: ddbbffc9-9788-4f5e-949f-1a13a22ae0be + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_1_sample_1_subject + identifier: + - value: 0e943de7-c277-48f2-8fa9-b2e836b03c2c + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_2_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_2_diagnosis_0 + identifier: + - value: 4c1cade2-18a6-4a2e-8264-949a3611fd88 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_2 + identifier: + - value: 1104505a-9890-49ce-8d7d-7a8070261324 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_2_sample_0 + identifier: + - value: 4dc515ba-6525-4619-8d57-520cc25f572e + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_2_sample_0_subject + identifier: + - value: 1104505a-9890-49ce-8d7d-7a8070261324 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_2_sample_1 + identifier: + - value: bc756b33-21bb-4f30-b32c-d899199b1927 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_2_sample_1_subject + identifier: + - value: 1104505a-9890-49ce-8d7d-7a8070261324 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_3_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_3_diagnosis_0 + identifier: + - value: e993cc6a-3774-4ef6-9f6a-77e9fe59c2a3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_3 + identifier: + - value: 195cd133-0d53-402d-b31c-3d4fe0481858 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_3_sample_0 + identifier: + - value: 5836c294-187d-4a17-96da-e1ee309ab854 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_3_sample_0_subject + identifier: + - value: 195cd133-0d53-402d-b31c-3d4fe0481858 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_3_sample_1 + identifier: + - value: a0b938d5-2cd5-4dbb-bb2a-d063cb6aceab + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_3_sample_1_subject + identifier: + - value: 195cd133-0d53-402d-b31c-3d4fe0481858 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_4_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_4_diagnosis_0 + identifier: + - value: 60422ff9-30a2-41da-ac80-7839e85c05c5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_4 + identifier: + - value: 1df726a4-8520-4474-8c00-d238a7384be1 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_4_sample_0 + identifier: + - value: 37d52145-52cc-40f9-8d6e-e13f3d1ed2f4 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_4_sample_0_subject + identifier: + - value: 1df726a4-8520-4474-8c00-d238a7384be1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_4_sample_1 + identifier: + - value: 4fc0fa56-50cd-42de-94cf-67a2f512ed3e + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_4_sample_1_subject + identifier: + - value: 1df726a4-8520-4474-8c00-d238a7384be1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_5_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_5_diagnosis_0 + identifier: + - value: 82901169-4165-40db-b88f-d9b2781a23d4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_5 + identifier: + - value: 2b4204ab-87af-4a79-913f-fabdcb2d02b4 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_5_sample_0 + identifier: + - value: cc407168-acf8-4123-a7a7-e6b178d60cad + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_5_sample_0_subject + identifier: + - value: 2b4204ab-87af-4a79-913f-fabdcb2d02b4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_5_sample_1 + identifier: + - value: d41e54ef-0167-47bf-acd1-2066cdc86f72 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_5_sample_1_subject + identifier: + - value: 2b4204ab-87af-4a79-913f-fabdcb2d02b4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_6_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_6_diagnosis_0 + identifier: + - value: 0833dc7e-0fbc-4ee5-8385-5329898e31a5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_6 + identifier: + - value: 3195cf36-998a-4f48-a7f1-a84f2b9fdcc5 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_6_sample_0 + identifier: + - value: 75383dbb-f784-4364-ae42-453dd65ba8e4 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_6_sample_0_subject + identifier: + - value: 3195cf36-998a-4f48-a7f1-a84f2b9fdcc5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_6_sample_1 + identifier: + - value: 87356cc6-6e50-4d47-ac12-b13db10b33f8 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_6_sample_1_subject + identifier: + - value: 3195cf36-998a-4f48-a7f1-a84f2b9fdcc5 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_7_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_7_diagnosis_0 + identifier: + - value: d82aa8ec-dd2b-4090-8b79-3e0956e42c42 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_7 + identifier: + - value: 37ea85c2-5e02-4d7c-846a-7cd40ef1912d + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_7_sample_0 + identifier: + - value: 86eaabba-4815-4768-8bf0-de382a14f780 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_7_sample_0_subject + identifier: + - value: 37ea85c2-5e02-4d7c-846a-7cd40ef1912d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_7_sample_1 + identifier: + - value: d4a2684e-4979-4e88-91c4-a465427b1efb + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_7_sample_1_subject + identifier: + - value: 37ea85c2-5e02-4d7c-846a-7cd40ef1912d + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_8_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_8_diagnosis_0 + identifier: + - value: 345d0762-8415-4ed0-82cc-9c53822f8207 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_8 + identifier: + - value: 3f8aba34-9229-4701-bd5d-869b3705d4a6 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_8_sample_0 + identifier: + - value: 108c405d-dda1-49e5-b0fa-2934997ab448 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_8_sample_0_subject + identifier: + - value: 3f8aba34-9229-4701-bd5d-869b3705d4a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_8_sample_1 + identifier: + - value: 833d168c-11fa-4019-a4d0-06769dc8cc3d + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_8_sample_1_subject + identifier: + - value: 3f8aba34-9229-4701-bd5d-869b3705d4a6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_9_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_9_diagnosis_0 + identifier: + - value: 519b1b07-fa20-4f9e-b576-a5013d464ce7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_9 + identifier: + - value: 4633e71f-5fbe-49b0-9721-9769182a08eb + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_9_sample_0 + identifier: + - value: 39002ad2-010e-43aa-b2fd-518cd3dae98f + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_9_sample_0_subject + identifier: + - value: 4633e71f-5fbe-49b0-9721-9769182a08eb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_9_sample_1 + identifier: + - value: c28ff0e8-87d0-4fae-b7a4-c3b420039b37 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_9_sample_1_subject + identifier: + - value: 4633e71f-5fbe-49b0-9721-9769182a08eb + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_10_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_10_diagnosis_0 + identifier: + - value: 2561b26f-3469-4687-9c16-a2fba97856da + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_10 + identifier: + - value: 482dd5ba-9c50-4ee3-a3f2-3bb0ad6487dc + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_10_sample_0 + identifier: + - value: 168a3751-fd92-4f33-a71f-86873aba0085 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_10_sample_0_subject + identifier: + - value: 482dd5ba-9c50-4ee3-a3f2-3bb0ad6487dc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_10_sample_1 + identifier: + - value: 4fc7835d-7cf4-48eb-85c7-56c401d3194e + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_10_sample_1_subject + identifier: + - value: 482dd5ba-9c50-4ee3-a3f2-3bb0ad6487dc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_11_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_11_diagnosis_0 + identifier: + - value: a971fb29-58a3-459e-a948-4b76a4727234 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_11 + identifier: + - value: 4c848c55-2c7e-4d32-9a17-b2531a18a19a + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_11_sample_0 + identifier: + - value: 1fbd56b5-807b-427b-8328-49a1715f6568 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_11_sample_0_subject + identifier: + - value: 4c848c55-2c7e-4d32-9a17-b2531a18a19a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_11_sample_1 + identifier: + - value: 485ec393-b13a-4b0e-80af-eea41c690f8e + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_11_sample_1_subject + identifier: + - value: 4c848c55-2c7e-4d32-9a17-b2531a18a19a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_12_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_12_diagnosis_0 + identifier: + - value: e32cee85-6d08-4a1b-8b87-30c6f1146273 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_12 + identifier: + - value: 58355fa4-e2ad-434b-a915-acbd09abbb77 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_12_sample_0 + identifier: + - value: afca2ecb-386a-4456-a3fc-f55720051dcd + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_12_sample_0_subject + identifier: + - value: 58355fa4-e2ad-434b-a915-acbd09abbb77 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_12_sample_1 + identifier: + - value: d46ac04c-fa07-4b95-9036-c85303548a2a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_12_sample_1_subject + identifier: + - value: 58355fa4-e2ad-434b-a915-acbd09abbb77 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_13_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_13_diagnosis_0 + identifier: + - value: b2311c0c-bbc1-4ff6-ae43-15162e0a5e36 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_13 + identifier: + - value: 59448f1d-6be8-466f-bb1a-1a3aef693d4f + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_13_sample_0 + identifier: + - value: 309a2bc8-64f7-4476-9ded-7f4ef3b56868 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_13_sample_0_subject + identifier: + - value: 59448f1d-6be8-466f-bb1a-1a3aef693d4f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_13_sample_1 + identifier: + - value: 4279459e-ff6f-4143-b7d3-2212c91e8179 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_13_sample_1_subject + identifier: + - value: 59448f1d-6be8-466f-bb1a-1a3aef693d4f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_14_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_14_diagnosis_0 + identifier: + - value: 449aa236-f610-48ab-8120-ae30cfe3f019 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_14 + identifier: + - value: 5e99d311-24f2-4ee5-abfe-c9d40771e8e3 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_14_sample_0 + identifier: + - value: ab9cc194-6571-411f-988e-d3c6387b2d00 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_14_sample_0_subject + identifier: + - value: 5e99d311-24f2-4ee5-abfe-c9d40771e8e3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_14_sample_1 + identifier: + - value: d12477a4-687d-4bfc-959a-9bac19c3f551 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_14_sample_1_subject + identifier: + - value: 5e99d311-24f2-4ee5-abfe-c9d40771e8e3 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_15_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_15_diagnosis_0 + identifier: + - value: fc81484a-469f-40b7-9a03-8ddcd1e4792f + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_15 + identifier: + - value: 6e4c8397-715c-4dc5-8782-2437ff207241 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_15_sample_0 + identifier: + - value: 1ed72838-8ce8-4e7e-91e4-0930747d12c3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_15_sample_0_subject + identifier: + - value: 6e4c8397-715c-4dc5-8782-2437ff207241 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_15_sample_1 + identifier: + - value: b9ab27c9-a1ac-4873-abc6-5edc0c20f623 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_15_sample_1_subject + identifier: + - value: 6e4c8397-715c-4dc5-8782-2437ff207241 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_16_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_16_diagnosis_0 + identifier: + - value: 3d23eadc-f1b3-4fb7-92ea-84aca053acc7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_16 + identifier: + - value: 71ebb445-ec2c-4ee1-aeaa-9cf30bb3bfff + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_16_sample_0 + identifier: + - value: 4debd1e2-e277-4b51-a068-ed33c30046d3 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_16_sample_0_subject + identifier: + - value: 71ebb445-ec2c-4ee1-aeaa-9cf30bb3bfff + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_16_sample_1 + identifier: + - value: bf58134f-46d8-49e2-99ff-395d7d6fac93 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_16_sample_1_subject + identifier: + - value: 71ebb445-ec2c-4ee1-aeaa-9cf30bb3bfff + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_17_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_17_diagnosis_0 + identifier: + - value: 3ec66f70-9f61-4209-87fc-fdada35dc4d1 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_17 + identifier: + - value: 7c02730b-5240-41ae-88b3-3f4e4514aa21 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_17_sample_0 + identifier: + - value: 0362992b-cc5b-4e58-b9c2-92df71f69e7b + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_17_sample_0_subject + identifier: + - value: 7c02730b-5240-41ae-88b3-3f4e4514aa21 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_17_sample_1 + identifier: + - value: 93bb269e-55ae-4dd0-97ef-4c4aea7583ba + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_17_sample_1_subject + identifier: + - value: 7c02730b-5240-41ae-88b3-3f4e4514aa21 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_18_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_18_diagnosis_0 + identifier: + - value: f61c22e7-85a4-48eb-9745-f8834747a807 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_18 + identifier: + - value: 7e16a4fa-3063-4ead-95e5-922f2cce6fac + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_18_sample_0 + identifier: + - value: 27276f1e-3665-4553-a0e6-03870e749ad2 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_18_sample_0_subject + identifier: + - value: 7e16a4fa-3063-4ead-95e5-922f2cce6fac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_18_sample_1 + identifier: + - value: 82fc8d50-9fe3-41d5-beeb-a094e13c8b67 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_18_sample_1_subject + identifier: + - value: 7e16a4fa-3063-4ead-95e5-922f2cce6fac + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_19_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_19_diagnosis_0 + identifier: + - value: f1e541b5-6256-4861-ab16-3c066f46b834 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_19 + identifier: + - value: 82b7bff1-63d8-47f3-8520-bee0c1b6b14e + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_19_sample_0 + identifier: + - value: 14b7f7dd-1ace-4a9a-920b-0c5697f070f5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_19_sample_0_subject + identifier: + - value: 82b7bff1-63d8-47f3-8520-bee0c1b6b14e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_19_sample_1 + identifier: + - value: b86bf2ab-25b3-43f1-94c4-4c0c4e1240e9 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_19_sample_1_subject + identifier: + - value: 82b7bff1-63d8-47f3-8520-bee0c1b6b14e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_20_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_20_diagnosis_0 + identifier: + - value: 37063e11-9833-4bbb-85e2-39d127122334 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_20 + identifier: + - value: 8369a540-474e-4b9b-8f2b-f96153ac8bfe + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_20_sample_0 + identifier: + - value: a14d3203-d84e-4b53-8a69-9c779f82e82f + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_20_sample_0_subject + identifier: + - value: 8369a540-474e-4b9b-8f2b-f96153ac8bfe + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_20_sample_1 + identifier: + - value: c999b871-d3bd-4a58-8070-c92c2ed48621 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_20_sample_1_subject + identifier: + - value: 8369a540-474e-4b9b-8f2b-f96153ac8bfe + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_21_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_21_diagnosis_0 + identifier: + - value: 2d2b34c9-20b0-47d0-a5e8-30db59d7d576 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_21 + identifier: + - value: 8782e6f7-d072-4107-8688-2289d001557a + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_21_sample_0 + identifier: + - value: 587cc557-a328-4b31-bab3-42b0d15d56c1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_21_sample_0_subject + identifier: + - value: 8782e6f7-d072-4107-8688-2289d001557a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_21_sample_1 + identifier: + - value: cdb9ec65-b4e4-4648-a86d-88f91de559c6 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_21_sample_1_subject + identifier: + - value: 8782e6f7-d072-4107-8688-2289d001557a + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_22_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_22_diagnosis_0 + identifier: + - value: e6285528-b535-4ed9-bf45-e342da3f95ca + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_22 + identifier: + - value: 8ac42bc3-472d-42e8-8455-09528a9977ea + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_22_sample_0 + identifier: + - value: 537409ca-df9e-4f83-87e3-172de75e78db + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_22_sample_0_subject + identifier: + - value: 8ac42bc3-472d-42e8-8455-09528a9977ea + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_22_sample_1 + identifier: + - value: 8967db82-c17a-4930-bcfb-f0ec48451493 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_22_sample_1_subject + identifier: + - value: 8ac42bc3-472d-42e8-8455-09528a9977ea + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_23_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_23_diagnosis_0 + identifier: + - value: 6405e77c-8d59-4cfd-8611-f9b07dfb3214 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_23 + identifier: + - value: 9548db2a-702d-46a0-8d02-bfdc497bdca8 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_23_sample_0 + identifier: + - value: 3f20aed6-bf3f-4265-829b-80348e501c81 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_23_sample_0_subject + identifier: + - value: 9548db2a-702d-46a0-8d02-bfdc497bdca8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_23_sample_1 + identifier: + - value: cda2c235-7673-482a-b35c-5089a08f91ec + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_23_sample_1_subject + identifier: + - value: 9548db2a-702d-46a0-8d02-bfdc497bdca8 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_24_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_24_diagnosis_0 + identifier: + - value: c7513c15-9434-44d0-b44c-d1232fb7c3ec + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_24 + identifier: + - value: 96fdbd9a-c9a5-4db9-8e0d-6ea200f975db + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_24_sample_0 + identifier: + - value: 259de38e-ff5a-483e-984a-039ff34a4e92 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_24_sample_0_subject + identifier: + - value: 96fdbd9a-c9a5-4db9-8e0d-6ea200f975db + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_24_sample_1 + identifier: + - value: 25b6989a-c23b-49c1-b169-372f142d7925 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_24_sample_1_subject + identifier: + - value: 96fdbd9a-c9a5-4db9-8e0d-6ea200f975db + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_25_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_25_diagnosis_0 + identifier: + - value: f4e75435-a0c2-4d97-86d5-054b5354b72b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_25 + identifier: + - value: 9bad78c0-6cb9-45bf-85e8-86cffe0b96fc + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_25_sample_0 + identifier: + - value: c9995f85-b7c8-4397-b43c-63ab923ecd87 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_25_sample_0_subject + identifier: + - value: 9bad78c0-6cb9-45bf-85e8-86cffe0b96fc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_25_sample_1 + identifier: + - value: e25c6504-b430-4419-9c72-39d0a37ab78b + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_25_sample_1_subject + identifier: + - value: 9bad78c0-6cb9-45bf-85e8-86cffe0b96fc + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_26_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_26_diagnosis_0 + identifier: + - value: 2ba21956-7dcb-4119-ad36-a815500f0a1b + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_26 + identifier: + - value: b2a945e3-e5cb-47d3-b74c-8bbf03fd33f2 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_26_sample_0 + identifier: + - value: 2bf29ef7-d9ec-41ee-be40-63832fc081c0 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_26_sample_0_subject + identifier: + - value: b2a945e3-e5cb-47d3-b74c-8bbf03fd33f2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_26_sample_1 + identifier: + - value: 793b9aaf-9d6a-4af4-aa4a-ec6d5882d0b1 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_26_sample_1_subject + identifier: + - value: b2a945e3-e5cb-47d3-b74c-8bbf03fd33f2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_27_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_27_diagnosis_0 + identifier: + - value: 9cbcacf8-7995-4187-824b-2e70616d3cc5 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_27 + identifier: + - value: b5988f8a-f71d-43f8-9474-51a8974e0bf7 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_27_sample_0 + identifier: + - value: 0872aa6f-e1e3-422f-9053-fce8a315b9ea + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_27_sample_0_subject + identifier: + - value: b5988f8a-f71d-43f8-9474-51a8974e0bf7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_27_sample_1 + identifier: + - value: 59d9977a-59c2-465c-88f5-1d69596aedca + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_27_sample_1_subject + identifier: + - value: b5988f8a-f71d-43f8-9474-51a8974e0bf7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_28_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_28_diagnosis_0 + identifier: + - value: dc28129c-7368-46e7-b54f-3aa345c23b26 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_28 + identifier: + - value: b9c7c8c2-271c-4eae-87f2-19a89b1ac58f + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_28_sample_0 + identifier: + - value: 3ebd62c9-5402-4d50-97eb-fc6a20e0ab43 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_28_sample_0_subject + identifier: + - value: b9c7c8c2-271c-4eae-87f2-19a89b1ac58f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_28_sample_1 + identifier: + - value: caa6a64e-b4f4-4fed-a980-ce3fc0ebc20e + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_28_sample_1_subject + identifier: + - value: b9c7c8c2-271c-4eae-87f2-19a89b1ac58f + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_29_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_29_diagnosis_0 + identifier: + - value: 8af84477-21a1-4b87-b5cf-e14538df503c + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_29 + identifier: + - value: c7a90e98-6f13-4480-8f69-74eea9e6efa6 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_29_sample_0 + identifier: + - value: b580b54a-1dd6-4ad1-910a-b2d581ff2787 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_29_sample_0_subject + identifier: + - value: c7a90e98-6f13-4480-8f69-74eea9e6efa6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_29_sample_1 + identifier: + - value: bab408b5-4498-4976-a7e6-92a898c9b926 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_29_sample_1_subject + identifier: + - value: c7a90e98-6f13-4480-8f69-74eea9e6efa6 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_30_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_30_diagnosis_0 + identifier: + - value: 0172f45e-6608-4627-a774-06837c68fa82 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_30 + identifier: + - value: ca087e3a-9e96-48e3-a28d-10bfaa39bcf1 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_30_sample_0 + identifier: + - value: 1fd1cc2c-73e1-4087-8387-aa8bf44b45b5 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_30_sample_0_subject + identifier: + - value: ca087e3a-9e96-48e3-a28d-10bfaa39bcf1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_30_sample_1 + identifier: + - value: 3a12f902-e54c-4144-84b3-766136b5c8b0 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_30_sample_1_subject + identifier: + - value: ca087e3a-9e96-48e3-a28d-10bfaa39bcf1 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_31_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_31_diagnosis_0 + identifier: + - value: 8da3d8bd-3efc-4651-a454-1c782ffbf9c3 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_31 + identifier: + - value: ced7d55d-fcb5-4b4a-8ba2-aaca18b958d7 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_31_sample_0 + identifier: + - value: 008cd82c-3d04-4b57-9fe2-f6e6c205d8a8 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_31_sample_0_subject + identifier: + - value: ced7d55d-fcb5-4b4a-8ba2-aaca18b958d7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_31_sample_1 + identifier: + - value: f403e032-4754-4749-9337-a3118ab49da0 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_31_sample_1_subject + identifier: + - value: ced7d55d-fcb5-4b4a-8ba2-aaca18b958d7 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_32_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_32_diagnosis_0 + identifier: + - value: caa8cf53-e54f-4810-87bb-b109ea7eed30 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_32 + identifier: + - value: d5b43f05-8489-44b4-8b3c-81a428f17fbd + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_32_sample_0 + identifier: + - value: 0380c374-1346-41bc-937f-1ab9a222c556 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_32_sample_0_subject + identifier: + - value: d5b43f05-8489-44b4-8b3c-81a428f17fbd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_32_sample_1 + identifier: + - value: 5303128f-5504-4b52-8d13-37818541fde4 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_32_sample_1_subject + identifier: + - value: d5b43f05-8489-44b4-8b3c-81a428f17fbd + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_33_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_33_diagnosis_0 + identifier: + - value: df516d7f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_33 + identifier: + - value: df4e907e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20653 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_33_sample_0 + identifier: + - value: df4f3418-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_33_sample_0_subject + identifier: + - value: df4e907e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_34_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_34_diagnosis_0 + identifier: + - value: df516f6b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_34 + identifier: + - value: df4e95d2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22430 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_34_sample_0 + identifier: + - value: df4f3614-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_34_sample_0_subject + identifier: + - value: df4e95d2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 400 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_35_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_35_diagnosis_0 + identifier: + - value: df51714a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_35 + identifier: + - value: df4e970b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18263 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_35_sample_0 + identifier: + - value: df4f373c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_35_sample_0_subject + identifier: + - value: df4e970b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 680 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_35_sample_1 + identifier: + - value: df4f391f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_35_sample_1_subject + identifier: + - value: df4e970b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 750 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_35_sample_2 + identifier: + - value: df4f3a47-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_35_sample_2_subject + identifier: + - value: df4e970b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 700 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_36_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_36_diagnosis_0 + identifier: + - value: df517351-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_36 + identifier: + - value: df4e9966-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20780 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_36_sample_0 + identifier: + - value: df4f3c26-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_36_sample_0_subject + identifier: + - value: df4e9966-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 300 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_36_sample_1 + identifier: + - value: df4f3d3f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_36_sample_1_subject + identifier: + - value: df4e9966-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 270 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_37_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_37_diagnosis_0 + identifier: + - value: df517547-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_37 + identifier: + - value: df4e9a58-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 17253 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_37_sample_0 + identifier: + - value: df4f3f1d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_37_sample_0_subject + identifier: + - value: df4e9a58-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 460 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_37_sample_1 + identifier: + - value: df4f4037-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_37_sample_1_subject + identifier: + - value: df4e9a58-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 130 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_38_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_38_diagnosis_0 + identifier: + - value: df51772f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_38 + identifier: + - value: df4e9b42-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20513 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_38_sample_0 + identifier: + - value: df4f4220-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_38_sample_0_subject + identifier: + - value: df4e9b42-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 250 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_38_sample_1 + identifier: + - value: df4f433c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_38_sample_1_subject + identifier: + - value: df4e9b42-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 750 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_39_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_39_diagnosis_0 + identifier: + - value: df51793e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_39 + identifier: + - value: df4e9d3d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22715 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_39_sample_0 + identifier: + - value: df4f453d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_39_sample_0_subject + identifier: + - value: df4e9d3d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 370 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_39_sample_1 + identifier: + - value: df4f4654-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_39_sample_1_subject + identifier: + - value: df4e9d3d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 250 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_40_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_40_diagnosis_0 + identifier: + - value: df517aae-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_40 + identifier: + - value: df4e9e22-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20956 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_40_sample_0 + identifier: + - value: df4f486a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_40_sample_0_subject + identifier: + - value: df4e9e22-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 290 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_40_sample_1 + identifier: + - value: df4f49cc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_40_sample_1_subject + identifier: + - value: df4e9e22-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 150 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_41_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_41_diagnosis_0 + identifier: + - value: df517c57-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_41 + identifier: + - value: df4e9ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23710 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_41_sample_0 + identifier: + - value: df4f4b89-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_41_sample_0_subject + identifier: + - value: df4e9ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 350 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_41_sample_1 + identifier: + - value: df4f4ca1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_41_sample_1_subject + identifier: + - value: df4e9ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 340 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_41_sample_2 + identifier: + - value: df4f4e74-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_41_sample_2_subject + identifier: + - value: df4e9ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 87 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_41_sample_3 + identifier: + - value: df4f4f98-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_41_sample_3_subject + identifier: + - value: df4e9ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 138 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_42_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_42_diagnosis_0 + identifier: + - value: df517d75-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_42 + identifier: + - value: df4ea101-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25156 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_42_sample_0 + identifier: + - value: df4f5158-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_42_sample_0_subject + identifier: + - value: df4ea101-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 660 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_42_sample_1 + identifier: + - value: df4f526b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_42_sample_1_subject + identifier: + - value: df4ea101-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 101 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_43_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_43_diagnosis_0 + identifier: + - value: df517fe1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_43 + identifier: + - value: df4ea1e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 29752 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_43_sample_0 + identifier: + - value: df4f5440-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_43_sample_0_subject + identifier: + - value: df4ea1e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 101 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_43_sample_1 + identifier: + - value: df4f555f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_43_sample_1_subject + identifier: + - value: df4ea1e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 50 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_44_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_44_diagnosis_0 + identifier: + - value: df518126-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_44 + identifier: + - value: df4ea3f5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20019 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_44_sample_0 + identifier: + - value: df4f577c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_44_sample_0_subject + identifier: + - value: df4ea3f5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 400 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_44_sample_1 + identifier: + - value: df4f58a8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_44_sample_1_subject + identifier: + - value: df4ea3f5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 660 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_45_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_45_diagnosis_0 + identifier: + - value: df5182e8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_45 + identifier: + - value: df4ea4dc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25290 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_45_sample_0 + identifier: + - value: df4f5a9b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_45_sample_0_subject + identifier: + - value: df4ea4dc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 220 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_46_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_46_diagnosis_0 + identifier: + - value: df51857b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_46 + identifier: + - value: df4ea7d8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22041 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_46_sample_0 + identifier: + - value: df4f5de7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_46_sample_0_subject + identifier: + - value: df4ea7d8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 150 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_46_sample_1 + identifier: + - value: df4f5ff9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_46_sample_1_subject + identifier: + - value: df4ea7d8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 114 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_47_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_47_diagnosis_0 + identifier: + - value: df51871d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_47 + identifier: + - value: df4ea9fe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 29749 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_47_sample_0 + identifier: + - value: df4f6161-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_47_sample_0_subject + identifier: + - value: df4ea9fe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 160 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_48_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_48_diagnosis_0 + identifier: + - value: df518844-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_48 + identifier: + - value: df4eaafe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22269 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_48_sample_0 + identifier: + - value: df4f6320-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_48_sample_0_subject + identifier: + - value: df4eaafe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 123 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_48_sample_1 + identifier: + - value: df4f6447-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_48_sample_1_subject + identifier: + - value: df4eaafe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 57 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_49_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_49_diagnosis_0 + identifier: + - value: df5189fa-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_49 + identifier: + - value: df4eac21-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23099 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_49_sample_0 + identifier: + - value: df4f6605-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_49_sample_0_subject + identifier: + - value: df4eac21-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 156 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_50_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_50_diagnosis_0 + identifier: + - value: df518cc8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_50 + identifier: + - value: df4eaeb4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23017 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_50_sample_0 + identifier: + - value: df4f68dd-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_50_sample_0_subject + identifier: + - value: df4eaeb4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 156 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_50_sample_1 + identifier: + - value: df4f69f2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_50_sample_1_subject + identifier: + - value: df4eaeb4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 84 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_51_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_51_diagnosis_0 + identifier: + - value: df518df3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_51 + identifier: + - value: df4eaf8f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19751 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_51_sample_0 + identifier: + - value: df4f6bc1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_51_sample_0_subject + identifier: + - value: df4eaf8f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 242 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_51_sample_1 + identifier: + - value: df4f6cd2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_51_sample_1_subject + identifier: + - value: df4eaf8f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 52 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_52_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_52_diagnosis_0 + identifier: + - value: df518f4f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_52 + identifier: + - value: df4eb063-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25254 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_52_sample_0 + identifier: + - value: df4f6eac-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_52_sample_0_subject + identifier: + - value: df4eb063-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 80 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_53_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_53_diagnosis_0 + identifier: + - value: df5190f6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_53 + identifier: + - value: df4eb20d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19881 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_53_sample_0 + identifier: + - value: df4f6fc0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_53_sample_0_subject + identifier: + - value: df4eb20d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 381 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_54_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_54_diagnosis_0 + identifier: + - value: df51920c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_54 + identifier: + - value: df4eb2e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18561 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_54_sample_0 + identifier: + - value: df4f71a3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_54_sample_0_subject + identifier: + - value: df4eb2e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 273 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_54_sample_1 + identifier: + - value: df4f72b9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_54_sample_1_subject + identifier: + - value: df4eb2e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 240 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_55_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_55_diagnosis_0 + identifier: + - value: df5193ba-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_55 + identifier: + - value: df4eb3f1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25727 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_55_sample_0 + identifier: + - value: df4f74af-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_55_sample_0_subject + identifier: + - value: df4eb3f1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 404 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_55_sample_1 + identifier: + - value: df4f76bb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_55_sample_1_subject + identifier: + - value: df4eb3f1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 460 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_56_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_56_diagnosis_0 + identifier: + - value: df5195ae-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_56 + identifier: + - value: df4eb5b7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23112 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_56_sample_0 + identifier: + - value: df4f7820-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_56_sample_0_subject + identifier: + - value: df4eb5b7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 78 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_56_sample_1 + identifier: + - value: df4f79d8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_56_sample_1_subject + identifier: + - value: df4eb5b7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 100 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_57_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_57_diagnosis_0 + identifier: + - value: df51982c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_57 + identifier: + - value: df4eb697-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24556 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_57_sample_0 + identifier: + - value: df4f7af4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_57_sample_0_subject + identifier: + - value: df4eb697-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 383 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_57_sample_1 + identifier: + - value: df4f7ca6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_57_sample_1_subject + identifier: + - value: df4eb697-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 380 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_58_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_58_diagnosis_0 + identifier: + - value: df5199b0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_58 + identifier: + - value: df4eb76a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19536 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_58_sample_0 + identifier: + - value: df4f7dc3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_58_sample_0_subject + identifier: + - value: df4eb76a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 226 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_59_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_59_diagnosis_0 + identifier: + - value: df519b17-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_59 + identifier: + - value: df4eb92f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19686 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_59_sample_0 + identifier: + - value: df4f7f88-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_59_sample_0_subject + identifier: + - value: df4eb92f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 161 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_60_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_60_diagnosis_0 + identifier: + - value: df519cc6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_60 + identifier: + - value: df4eba07-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24489 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_60_sample_0 + identifier: + - value: df4f80a8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_60_sample_0_subject + identifier: + - value: df4eba07-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 264 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_61_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_61_diagnosis_0 + identifier: + - value: df519de4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_61 + identifier: + - value: df4ebbd7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19384 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_61_sample_0 + identifier: + - value: df4f8281-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_61_sample_0_subject + identifier: + - value: df4ebbd7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 89 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_61_sample_1 + identifier: + - value: df4f8393-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_61_sample_1_subject + identifier: + - value: df4ebbd7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 137 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_62_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_62_diagnosis_0 + identifier: + - value: df519f90-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_62 + identifier: + - value: df4ebcaf-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24608 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_62_sample_0 + identifier: + - value: df4f856c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_62_sample_0_subject + identifier: + - value: df4ebcaf-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 300 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_63_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_63_diagnosis_0 + identifier: + - value: df51a0ab-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_63 + identifier: + - value: df4ebebb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23545 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_63_sample_0 + identifier: + - value: df4f8687-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_63_sample_0_subject + identifier: + - value: df4ebebb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 90 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_63_sample_1 + identifier: + - value: df4f8873-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_63_sample_1_subject + identifier: + - value: df4ebebb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 71 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_64_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_64_diagnosis_0 + identifier: + - value: df51a339-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_64 + identifier: + - value: df4ebfa3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21468 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_64_sample_0 + identifier: + - value: df4f8990-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_64_sample_0_subject + identifier: + - value: df4ebfa3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 158 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_65_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_65_diagnosis_0 + identifier: + - value: df51a495-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_65 + identifier: + - value: df4ec190-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19312 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_65_sample_0 + identifier: + - value: df4f8b7d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_65_sample_0_subject + identifier: + - value: df4ec190-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 126 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_65_sample_1 + identifier: + - value: df4f8dc3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_65_sample_1_subject + identifier: + - value: df4ec190-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 257 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_66_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_66_diagnosis_0 + identifier: + - value: df51a600-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_66 + identifier: + - value: df4ec26a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18322 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_66_sample_0 + identifier: + - value: df4f8f32-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_66_sample_0_subject + identifier: + - value: df4ec26a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 123 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_66_sample_1 + identifier: + - value: df4f90f5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_66_sample_1_subject + identifier: + - value: df4ec26a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 139 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_67_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_67_diagnosis_0 + identifier: + - value: df51a7b7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_67 + identifier: + - value: df4ec459-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25041 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_67_sample_0 + identifier: + - value: df4f92c1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_67_sample_0_subject + identifier: + - value: df4ec459-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 14 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_68_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_68_diagnosis_0 + identifier: + - value: df51a8fb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_68 + identifier: + - value: df4ec539-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26376 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_68_sample_0 + identifier: + - value: df4f949e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_68_sample_0_subject + identifier: + - value: df4ec539-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 169 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_68_sample_1 + identifier: + - value: df4f95b6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_68_sample_1_subject + identifier: + - value: df4ec539-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 127 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_69_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_69_diagnosis_0 + identifier: + - value: df51aabd-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_69 + identifier: + - value: df4ec739-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20774 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_69_sample_0 + identifier: + - value: df4f977a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_69_sample_0_subject + identifier: + - value: df4ec739-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 137 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_69_sample_1 + identifier: + - value: df4f988c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_69_sample_1_subject + identifier: + - value: df4ec739-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 57 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_70_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_70_diagnosis_0 + identifier: + - value: df51abd9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_70 + identifier: + - value: df4ec812-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24920 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_70_sample_0 + identifier: + - value: df4f9a54-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_70_sample_0_subject + identifier: + - value: df4ec812-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 177 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_71_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_71_diagnosis_0 + identifier: + - value: df51ad8e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_71 + identifier: + - value: df4eca22-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26258 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_71_sample_0 + identifier: + - value: df4f9b69-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_71_sample_0_subject + identifier: + - value: df4eca22-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 213 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_71_sample_1 + identifier: + - value: df4f9d3a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_71_sample_1_subject + identifier: + - value: df4eca22-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 98 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_72_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_72_diagnosis_0 + identifier: + - value: df51aeca-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_72 + identifier: + - value: df4ecafb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26753 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_72_sample_0 + identifier: + - value: df4f9e53-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_72_sample_0_subject + identifier: + - value: df4ecafb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 205 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_73_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_73_diagnosis_0 + identifier: + - value: df51b035-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_73 + identifier: + - value: df4ecd30-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23404 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_73_sample_0 + identifier: + - value: df4fa031-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_73_sample_0_subject + identifier: + - value: df4ecd30-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 75 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_73_sample_1 + identifier: + - value: df4fa14c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_73_sample_1_subject + identifier: + - value: df4ecd30-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 216 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_74_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_74_diagnosis_0 + identifier: + - value: df51b1e3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_74 + identifier: + - value: df4ece54-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24868 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_74_sample_0 + identifier: + - value: df4fa33f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_74_sample_0_subject + identifier: + - value: df4ece54-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 197 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_75_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_75_diagnosis_0 + identifier: + - value: df51b303-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_75 + identifier: + - value: df4ecf32-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22915 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_75_sample_0 + identifier: + - value: df4fa54a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_75_sample_0_subject + identifier: + - value: df4ecf32-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 280 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_75_sample_1 + identifier: + - value: df4fa6c0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_75_sample_1_subject + identifier: + - value: df4ecf32-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 128 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_76_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_76_diagnosis_0 + identifier: + - value: df51b5b0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_76 + identifier: + - value: df4ed0d5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23506 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_76_sample_0 + identifier: + - value: df4fa881-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_76_sample_0_subject + identifier: + - value: df4ed0d5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_76_sample_1 + identifier: + - value: df4fa99b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_76_sample_1_subject + identifier: + - value: df4ed0d5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 80 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_77_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_77_diagnosis_0 + identifier: + - value: df51b6f3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_77 + identifier: + - value: df4ed1b2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21708 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_77_sample_0 + identifier: + - value: df4fab53-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_77_sample_0_subject + identifier: + - value: df4ed1b2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 164 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_77_sample_1 + identifier: + - value: df4fac69-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_77_sample_1_subject + identifier: + - value: df4ed1b2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 73 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_78_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_78_diagnosis_0 + identifier: + - value: df51b8b0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_78 + identifier: + - value: df4ed282-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22982 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_78_sample_0 + identifier: + - value: df4fae2e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_78_sample_0_subject + identifier: + - value: df4ed282-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 163 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_78_sample_1 + identifier: + - value: df4faf3f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_78_sample_1_subject + identifier: + - value: df4ed282-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 82 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_79_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_79_diagnosis_0 + identifier: + - value: df51b9ed-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_79 + identifier: + - value: df4ed42c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24594 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_79_sample_0 + identifier: + - value: df4fb0fc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_79_sample_0_subject + identifier: + - value: df4ed42c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 271 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_79_sample_1 + identifier: + - value: df4fb20a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_79_sample_1_subject + identifier: + - value: df4ed42c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 50 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_80_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_80_diagnosis_0 + identifier: + - value: df51bb53-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_80 + identifier: + - value: df4ed504-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23038 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_80_sample_0 + identifier: + - value: df4fb3e3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_80_sample_0_subject + identifier: + - value: df4ed504-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_80_sample_1 + identifier: + - value: df4fb4fa-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_80_sample_1_subject + identifier: + - value: df4ed504-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 141 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_81_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_81_diagnosis_0 + identifier: + - value: df51bd00-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_81 + identifier: + - value: df4ed5d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24082 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_81_sample_0 + identifier: + - value: df4fb6da-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_81_sample_0_subject + identifier: + - value: df4ed5d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 221 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_81_sample_1 + identifier: + - value: df4fb7f3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_81_sample_1_subject + identifier: + - value: df4ed5d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_82_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_82_diagnosis_0 + identifier: + - value: df51be1b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_82 + identifier: + - value: df4ed786-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22403 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_82_sample_0 + identifier: + - value: df4fb9da-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_82_sample_0_subject + identifier: + - value: df4ed786-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 133 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_83_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_83_diagnosis_0 + identifier: + - value: df51bfcc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_83 + identifier: + - value: df4ed85e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23694 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_83_sample_0 + identifier: + - value: df4fbbea-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_83_sample_0_subject + identifier: + - value: df4ed85e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 218 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_83_sample_1 + identifier: + - value: df4fbd53-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_83_sample_1_subject + identifier: + - value: df4ed85e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 134 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_84_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_84_diagnosis_0 + identifier: + - value: df51c0f4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_84 + identifier: + - value: df4eda1a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18216 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_84_sample_0 + identifier: + - value: df4fbf1d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_84_sample_0_subject + identifier: + - value: df4eda1a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 207 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_84_sample_1 + identifier: + - value: df4fc033-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_84_sample_1_subject + identifier: + - value: df4eda1a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 221 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_85_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_85_diagnosis_0 + identifier: + - value: df51c2ac-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_85 + identifier: + - value: df4edaf6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20359 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_85_sample_0 + identifier: + - value: df4fc20a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_85_sample_0_subject + identifier: + - value: df4edaf6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 208 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_86_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_86_diagnosis_0 + identifier: + - value: df51c3e5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_86 + identifier: + - value: df4edcd7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25376 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_86_sample_0 + identifier: + - value: df4fc332-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_86_sample_0_subject + identifier: + - value: df4edcd7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 207 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_86_sample_1 + identifier: + - value: df4fc505-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_86_sample_1_subject + identifier: + - value: df4edcd7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 198 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_87_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_87_diagnosis_0 + identifier: + - value: df51c53b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_87 + identifier: + - value: df4eddbb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21586 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_87_sample_0 + identifier: + - value: df4fc613-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_87_sample_0_subject + identifier: + - value: df4eddbb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 245 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_87_sample_1 + identifier: + - value: df4fc7e1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_87_sample_1_subject + identifier: + - value: df4eddbb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 138 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_88_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_88_diagnosis_0 + identifier: + - value: df51c6e6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_88 + identifier: + - value: df4edf88-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22285 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_88_sample_0 + identifier: + - value: df4fc902-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_88_sample_0_subject + identifier: + - value: df4edf88-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 440 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_89_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_89_diagnosis_0 + identifier: + - value: df51c808-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_89 + identifier: + - value: df4ee063-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 15703 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_89_sample_0 + identifier: + - value: df4fcada-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_89_sample_0_subject + identifier: + - value: df4ee063-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 199 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_89_sample_1 + identifier: + - value: df4fcbfb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_89_sample_1_subject + identifier: + - value: df4ee063-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 51 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_90_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_90_diagnosis_0 + identifier: + - value: df51c9af-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_90 + identifier: + - value: df4ee240-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21257 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_90_sample_0 + identifier: + - value: df4fcdf1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_90_sample_0_subject + identifier: + - value: df4ee240-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 76 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_91_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_91_diagnosis_0 + identifier: + - value: df51cac8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_91 + identifier: + - value: df4ee338-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 16652 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_91_sample_0 + identifier: + - value: df4fcf01-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_91_sample_0_subject + identifier: + - value: df4ee338-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 101 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_92_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_92_diagnosis_0 + identifier: + - value: df51cc89-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_92 + identifier: + - value: df4ee534-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 29529 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_92_sample_0 + identifier: + - value: df4fd0ef-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_92_sample_0_subject + identifier: + - value: df4ee534-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 150 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_93_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_93_diagnosis_0 + identifier: + - value: df51cdbe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_93 + identifier: + - value: df4ee623-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23707 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_93_sample_0 + identifier: + - value: df4fd2ff-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_93_sample_0_subject + identifier: + - value: df4ee623-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 250 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_93_sample_1 + identifier: + - value: df4fd453-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_93_sample_1_subject + identifier: + - value: df4ee623-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 270 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_94_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_94_diagnosis_0 + identifier: + - value: df51cf25-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_94 + identifier: + - value: df4ee821-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 8551 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_94_sample_0 + identifier: + - value: df4fd60a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_94_sample_0_subject + identifier: + - value: df4ee821-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 380 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_94_sample_1 + identifier: + - value: df4fd726-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_94_sample_1_subject + identifier: + - value: df4ee821-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 400 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_95_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_95_diagnosis_0 + identifier: + - value: df51d0d0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_95 + identifier: + - value: df4ee8fe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 28077 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_95_sample_0 + identifier: + - value: df4fd8e9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_95_sample_0_subject + identifier: + - value: df4ee8fe-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 190 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_96_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_96_diagnosis_0 + identifier: + - value: df51d1ea-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_96 + identifier: + - value: df4eeb29-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18210 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_96_sample_0 + identifier: + - value: df4fda01-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_96_sample_0_subject + identifier: + - value: df4eeb29-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 300 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_97_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_97_diagnosis_0 + identifier: + - value: df51d3cf-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_97 + identifier: + - value: df4eec12-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 14629 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_97_sample_0 + identifier: + - value: df4fdbca-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_97_sample_0_subject + identifier: + - value: df4eec12-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 107 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_98_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_98_diagnosis_0 + identifier: + - value: df51d4f9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_98 + identifier: + - value: df4eee28-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25138 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_98_sample_0 + identifier: + - value: df4fdce6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_98_sample_0_subject + identifier: + - value: df4eee28-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 247 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_99_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_99_diagnosis_0 + identifier: + - value: df51d6b6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_99 + identifier: + - value: df4eef1c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23789 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_99_sample_0 + identifier: + - value: df4fdeb5-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_99_sample_0_subject + identifier: + - value: df4eef1c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 132 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_99_sample_1 + identifier: + - value: df4fdfd2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_99_sample_1_subject + identifier: + - value: df4eef1c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 104 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_100_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_100_diagnosis_0 + identifier: + - value: df51d7fd-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_100 + identifier: + - value: df4ef039-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21529 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_100_sample_0 + identifier: + - value: df4fe1b4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_100_sample_0_subject + identifier: + - value: df4ef039-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 55 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_101_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_101_diagnosis_0 + identifier: + - value: df51dc2f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_101 + identifier: + - value: df4ef10e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22872 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_101_sample_0 + identifier: + - value: df4fe2c7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_101_sample_0_subject + identifier: + - value: df4ef10e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 65 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_101_sample_1 + identifier: + - value: df4fe4ae-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_101_sample_1_subject + identifier: + - value: df4ef10e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 91 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_102_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_102_diagnosis_0 + identifier: + - value: df51de2e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_102 + identifier: + - value: df4ef2ab-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26252 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_102_sample_0 + identifier: + - value: df4fe5c9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_102_sample_0_subject + identifier: + - value: df4ef2ab-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 237 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_102_sample_1 + identifier: + - value: df4fe7c6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_102_sample_1_subject + identifier: + - value: df4ef2ab-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 85 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_103_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_103_diagnosis_0 + identifier: + - value: df51df84-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_103 + identifier: + - value: df4ef386-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21782 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_103_sample_0 + identifier: + - value: df4fe9e1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_103_sample_0_subject + identifier: + - value: df4ef386-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 170 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_103_sample_1 + identifier: + - value: df4feb43-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_103_sample_1_subject + identifier: + - value: df4ef386-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 97 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_104_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_104_diagnosis_0 + identifier: + - value: df51e14d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_104 + identifier: + - value: df4ef458-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22292 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_104_sample_0 + identifier: + - value: df4fed08-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_104_sample_0_subject + identifier: + - value: df4ef458-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 137 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_104_sample_1 + identifier: + - value: df4fee1e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_104_sample_1_subject + identifier: + - value: df4ef458-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 142 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_105_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_105_diagnosis_0 + identifier: + - value: df51e278-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_105 + identifier: + - value: df4ef6b1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23896 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_105_sample_0 + identifier: + - value: df4fefd8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_105_sample_0_subject + identifier: + - value: df4ef6b1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 170 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_105_sample_1 + identifier: + - value: df4ff0e6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_105_sample_1_subject + identifier: + - value: df4ef6b1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 317 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_106_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_106_diagnosis_0 + identifier: + - value: df51e439-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_106 + identifier: + - value: df4ef7ac-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21881 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_106_sample_0 + identifier: + - value: df4ff2b1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_106_sample_0_subject + identifier: + - value: df4ef7ac-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 214 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_106_sample_1 + identifier: + - value: df4ff3b8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_106_sample_1_subject + identifier: + - value: df4ef7ac-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 206 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_107_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_107_diagnosis_0 + identifier: + - value: df51e57c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_107 + identifier: + - value: df4ef87b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24572 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_107_sample_0 + identifier: + - value: df4ff584-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_107_sample_0_subject + identifier: + - value: df4ef87b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 215 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_107_sample_1 + identifier: + - value: df4ff693-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_107_sample_1_subject + identifier: + - value: df4ef87b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 156 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_108_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_108_diagnosis_0 + identifier: + - value: df51e6f1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_108 + identifier: + - value: df4efa74-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 28410 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_108_sample_0 + identifier: + - value: df4ff8a0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_108_sample_0_subject + identifier: + - value: df4efa74-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 125 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_108_sample_1 + identifier: + - value: df4ff9c7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_108_sample_1_subject + identifier: + - value: df4efa74-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 106 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_109_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_109_diagnosis_0 + identifier: + - value: df51e8a4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_109 + identifier: + - value: df4efb5a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19938 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_109_sample_0 + identifier: + - value: df4ffbb7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_109_sample_0_subject + identifier: + - value: df4efb5a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 460 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_110_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_110_diagnosis_0 + identifier: + - value: df51e9c8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_110 + identifier: + - value: df4efd1a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 28032 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_110_sample_0 + identifier: + - value: df4ffcc6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_110_sample_0_subject + identifier: + - value: df4efd1a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 163 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_111_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_111_diagnosis_0 + identifier: + - value: df51eb8a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_111 + identifier: + - value: df4efdf1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23616 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_111_sample_0 + identifier: + - value: df4ffeb8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_111_sample_0_subject + identifier: + - value: df4efdf1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 273 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_112_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_112_diagnosis_0 + identifier: + - value: df51ecb4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_112 + identifier: + - value: df4effbc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26052 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_112_sample_0 + identifier: + - value: df4fffe4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_112_sample_0_subject + identifier: + - value: df4effbc-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 135 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_113_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_113_diagnosis_0 + identifier: + - value: df51ee7b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_113 + identifier: + - value: df4f0094-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25648 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_113_sample_0 + identifier: + - value: df50013e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_113_sample_0_subject + identifier: + - value: df4f0094-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 239 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_114_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_114_diagnosis_0 + identifier: + - value: df51efb6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_114 + identifier: + - value: df4f0263-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19702 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_114_sample_0 + identifier: + - value: df5002fa-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_114_sample_0_subject + identifier: + - value: df4f0263-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 190 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_115_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_115_diagnosis_0 + identifier: + - value: df51f135-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_115 + identifier: + - value: df4f0338-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23634 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_115_sample_0 + identifier: + - value: df500413-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_115_sample_0_subject + identifier: + - value: df4f0338-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 190 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_115_sample_1 + identifier: + - value: df5005c8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_115_sample_1_subject + identifier: + - value: df4f0338-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_116_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_116_diagnosis_0 + identifier: + - value: df51f2f0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_116 + identifier: + - value: df4f0514-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23729 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_116_sample_0 + identifier: + - value: df5006db-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_116_sample_0_subject + identifier: + - value: df4f0514-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 320 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_116_sample_1 + identifier: + - value: df50089f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_116_sample_1_subject + identifier: + - value: df4f0514-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 320 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_117_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_117_diagnosis_0 + identifier: + - value: df51f418-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_117 + identifier: + - value: df4f05ee-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18832 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_117_sample_0 + identifier: + - value: df5009af-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_117_sample_0_subject + identifier: + - value: df4f05ee-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 350 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_117_sample_1 + identifier: + - value: df500b7f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_117_sample_1_subject + identifier: + - value: df4f05ee-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_118_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_118_diagnosis_0 + identifier: + - value: df51f5cf-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_118 + identifier: + - value: df4f07d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21757 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_118_sample_0 + identifier: + - value: df500c9a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_118_sample_0_subject + identifier: + - value: df4f07d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 460 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_118_sample_1 + identifier: + - value: df500e73-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_118_sample_1_subject + identifier: + - value: df4f07d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 280 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_119_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_119_diagnosis_0 + identifier: + - value: df51f6eb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_119 + identifier: + - value: df4f08ad-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22641 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_119_sample_0 + identifier: + - value: df500f8c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_119_sample_0_subject + identifier: + - value: df4f08ad-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 290 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_119_sample_1 + identifier: + - value: df50116d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_119_sample_1_subject + identifier: + - value: df4f08ad-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 420 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_120_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_120_diagnosis_0 + identifier: + - value: df51f8b7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_120 + identifier: + - value: df4f0a9f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21361 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_120_sample_0 + identifier: + - value: df501289-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_120_sample_0_subject + identifier: + - value: df4f0a9f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 220 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_121_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_121_diagnosis_0 + identifier: + - value: df51f9e7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_121 + identifier: + - value: df4f0b7a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24899 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_121_sample_0 + identifier: + - value: df501477-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_121_sample_0_subject + identifier: + - value: df4f0b7a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 184 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_121_sample_1 + identifier: + - value: df501689-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_121_sample_1_subject + identifier: + - value: df4f0b7a-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 116 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_122_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_122_diagnosis_0 + identifier: + - value: df51fb62-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_122 + identifier: + - value: df4f0d7f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 18540 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_122_sample_0 + identifier: + - value: df5017ed-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_122_sample_0_subject + identifier: + - value: df4f0d7f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 134 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_123_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_123_diagnosis_0 + identifier: + - value: df51fd19-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_123 + identifier: + - value: df4f0e55-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24500 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_123_sample_0 + identifier: + - value: df5019a0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_123_sample_0_subject + identifier: + - value: df4f0e55-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 259 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_124_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_124_diagnosis_0 + identifier: + - value: df51ff4e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_124 + identifier: + - value: df4f1067-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24203 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_124_sample_0 + identifier: + - value: df501ab6-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_124_sample_0_subject + identifier: + - value: df4f1067-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 152 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_125_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_125_diagnosis_0 + identifier: + - value: df520120-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_125 + identifier: + - value: df4f1155-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19778 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_125_sample_0 + identifier: + - value: df501c70-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_125_sample_0_subject + identifier: + - value: df4f1155-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 185 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_125_sample_1 + identifier: + - value: df501d83-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_125_sample_1_subject + identifier: + - value: df4f1155-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 115 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_126_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_126_diagnosis_0 + identifier: + - value: df520249-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_126 + identifier: + - value: df4f1268-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21732 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_126_sample_0 + identifier: + - value: df501f47-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_126_sample_0_subject + identifier: + - value: df4f1268-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 112 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_126_sample_1 + identifier: + - value: df502056-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_126_sample_1_subject + identifier: + - value: df4f1268-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 123 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_127_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_127_diagnosis_0 + identifier: + - value: df5204d4-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_127 + identifier: + - value: df4f1344-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20363 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_127_sample_0 + identifier: + - value: df502226-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_127_sample_0_subject + identifier: + - value: df4f1344-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 88 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_127_sample_1 + identifier: + - value: df502332-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_127_sample_1_subject + identifier: + - value: df4f1344-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 87 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_128_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_128_diagnosis_0 + identifier: + - value: df520657-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_128 + identifier: + - value: df4f14e8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 23849 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_128_sample_0 + identifier: + - value: df50250d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_128_sample_0_subject + identifier: + - value: df4f14e8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 96 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_128_sample_1 + identifier: + - value: df502618-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_128_sample_1_subject + identifier: + - value: df4f14e8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 97 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_129_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_129_diagnosis_0 + identifier: + - value: df5207ce-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_129 + identifier: + - value: df4f15be-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19338 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_129_sample_0 + identifier: + - value: df5027fb-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_129_sample_0_subject + identifier: + - value: df4f15be-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 81 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_129_sample_1 + identifier: + - value: df502909-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_129_sample_1_subject + identifier: + - value: df4f15be-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 99 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_130_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_130_diagnosis_0 + identifier: + - value: df520983-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_130 + identifier: + - value: df4f1689-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 21474 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_130_sample_0 + identifier: + - value: df502af8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_130_sample_0_subject + identifier: + - value: df4f1689-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 160 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_130_sample_1 + identifier: + - value: df502d00-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_130_sample_1_subject + identifier: + - value: df4f1689-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 190 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_131_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_131_diagnosis_0 + identifier: + - value: df520aac-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_131 + identifier: + - value: df4f1830-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19505 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_131_sample_0 + identifier: + - value: df502f10-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_131_sample_0_subject + identifier: + - value: df4f1830-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 380 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_132_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_132_diagnosis_0 + identifier: + - value: df520c6b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_132 + identifier: + - value: df4f1907-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22113 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_132_sample_0 + identifier: + - value: df5030f2-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_132_sample_0_subject + identifier: + - value: df4f1907-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 320 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_132_sample_1 + identifier: + - value: df503207-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_132_sample_1_subject + identifier: + - value: df4f1907-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 380 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_133_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_133_diagnosis_0 + identifier: + - value: df520d93-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_133 + identifier: + - value: df4f19d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 25635 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_133_sample_0 + identifier: + - value: df5033be-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_133_sample_0_subject + identifier: + - value: df4f19d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 200 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_133_sample_1 + identifier: + - value: df5034c7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_133_sample_1_subject + identifier: + - value: df4f19d3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 350 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_134_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_134_diagnosis_0 + identifier: + - value: df520f60-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_134 + identifier: + - value: df4f1b8c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 19705 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_134_sample_0 + identifier: + - value: df503688-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_134_sample_0_subject + identifier: + - value: df4f1b8c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 370 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_135_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_135_diagnosis_0 + identifier: + - value: df5210a0-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_135 + identifier: + - value: df4f1c60-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26874 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_135_sample_0 + identifier: + - value: df50379b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_135_sample_0_subject + identifier: + - value: df4f1c60-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 77 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_136_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_136_diagnosis_0 + identifier: + - value: df52120e-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_136 + identifier: + - value: df4f1d2d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 22645 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_136_sample_0 + identifier: + - value: df503973-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_136_sample_0_subject + identifier: + - value: df4f1d2d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 129 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_136_sample_1 + identifier: + - value: df503a8f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_136_sample_1_subject + identifier: + - value: df4f1d2d-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 88 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_137_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_137_diagnosis_0 + identifier: + - value: df5213c1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_137 + identifier: + - value: df4f1ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24876 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_137_sample_0 + identifier: + - value: df503c6f-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_137_sample_0_subject + identifier: + - value: df4f1ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 210 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_137_sample_1 + identifier: + - value: df503d83-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_137_sample_1_subject + identifier: + - value: df4f1ef8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 27 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_138_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_138_diagnosis_0 + identifier: + - value: df521517-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_138 + identifier: + - value: df4f1fff-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26445 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_138_sample_0 + identifier: + - value: df503f6c-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_138_sample_0_subject + identifier: + - value: df4f1fff-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 131 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_138_sample_1 + identifier: + - value: df504083-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_138_sample_1_subject + identifier: + - value: df4f1fff-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 126 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_139_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_139_diagnosis_0 + identifier: + - value: df521955-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_139 + identifier: + - value: df4f20dd-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 26252 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_139_sample_0 + identifier: + - value: df504274-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_139_sample_0_subject + identifier: + - value: df4f20dd-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 263 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_139_sample_1 + identifier: + - value: df504484-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_139_sample_1_subject + identifier: + - value: df4f20dd-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 241 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_140_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_140_diagnosis_0 + identifier: + - value: df521ac9-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_140 + identifier: + - value: df4f22b3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24049 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_140_sample_0 + identifier: + - value: df5045ea-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_140_sample_0_subject + identifier: + - value: df4f22b3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 229 + unit: + coding: &id001 + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_140_sample_1 + identifier: + - value: df5047ab-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_140_sample_1_subject + identifier: + - value: df4f22b3-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 37 + unit: + coding: *id001 + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_141_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_141_diagnosis_0 + identifier: + - value: df521ca7-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_141 + identifier: + - value: df4f238b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 24126 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_141_sample_0 + identifier: + - value: df5048c8-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_141_sample_0_subject + identifier: + - value: df4f238b-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 146 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_142_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_142_diagnosis_0 + identifier: + - value: df521df1-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_142 + identifier: + - value: df4f2567-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + age_at_diagnosis: + value_decimal: 20250 + unit: + coding: + - code: C25301 + system: http://ncithesaurus.nci.nih.gov + label: Day + tag: + - harmonized + condition: + coding: + - code: Squamous cell carcinoma, NOS + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: 8070/3 + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_142_sample_0 + identifier: + - value: df504a87-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_142_sample_0_subject + identifier: + - value: df4f2567-8f98-11ea-b1fd-0aad30af8a83 + system: http://crdc.nci.nih.gov/gdc#case_id + creation_activity: + quantity_collected: + value_decimal: 1390 + unit: + coding: + - code: C28253 + system: http://ncithesaurus.nci.nih.gov + label: Milligram + tag: + - harmonized + processing_activity: + - activity_type: + coding: + - code: Snap Frozen + system: http://crdc.nci.nih.gov/gdc + method_type: + coding: + - code: LN2 + system: http://crdc.nci.nih.gov/gdc + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_143_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_143_diagnosis_0 + identifier: + - value: aa24d55d-9793-4d25-ba17-1629ba8d605a + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_143 + identifier: + - value: df6bef95-c233-4b10-b321-36ef4e79b5d4 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_143_sample_0 + identifier: + - value: 1c1d1b89-142a-4d11-acd7-453162134116 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_143_sample_0_subject + identifier: + - value: df6bef95-c233-4b10-b321-36ef4e79b5d4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_143_sample_1 + identifier: + - value: 6ae86730-dda1-43a0-90ec-ddec4d467846 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_143_sample_1_subject + identifier: + - value: df6bef95-c233-4b10-b321-36ef4e79b5d4 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_144_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_144_diagnosis_0 + identifier: + - value: ecee1b49-6b8f-4914-8a39-8a505a4ac204 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_144 + identifier: + - value: e11e9155-4ac6-43dc-b8e5-1be822cd2dab + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_144_sample_0 + identifier: + - value: c95750b7-ef96-4f6c-a0ae-e0ba4735414e + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_144_sample_0_subject + identifier: + - value: e11e9155-4ac6-43dc-b8e5-1be822cd2dab + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_144_sample_1 + identifier: + - value: fe9556eb-1ad4-45b6-b78f-dd29cca9ed20 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_144_sample_1_subject + identifier: + - value: e11e9155-4ac6-43dc-b8e5-1be822cd2dab + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_145_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_145_diagnosis_0 + identifier: + - value: e8adcdcd-36d4-444e-9c83-d9fe640dd5b4 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_145 + identifier: + - value: ea7c9fbd-8353-4f3c-9fea-2fba79140536 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_145_sample_0 + identifier: + - value: ba497617-aba1-4037-90f7-fc2c66ad10dd + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_145_sample_0_subject + identifier: + - value: ea7c9fbd-8353-4f3c-9fea-2fba79140536 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_145_sample_1 + identifier: + - value: dcc22b0d-0018-4601-b8ba-bbeab30ab624 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_145_sample_1_subject + identifier: + - value: ea7c9fbd-8353-4f3c-9fea-2fba79140536 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_146_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_146_diagnosis_0 + identifier: + - value: be6c0a43-9ca3-4b25-bc58-d2bc278642e7 + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_146 + identifier: + - value: f581075d-1b69-4812-9fe4-2bde4aad8bf2 + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_146_sample_0 + identifier: + - value: 2fee1b7b-3c77-41e5-9bfe-f46e224a629a + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_146_sample_0_subject + identifier: + - value: f581075d-1b69-4812-9fe4-2bde4aad8bf2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_146_sample_1 + identifier: + - value: 90bfa434-2fd6-4a5f-b03e-551bb0440022 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_146_sample_1_subject + identifier: + - value: f581075d-1b69-4812-9fe4-2bde4aad8bf2 + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc +--- +pdc_head_and_mouth_example_147_diagnosis_0_diagnosis: + Provenance: Downloaded from the GDC Public API (see https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb + for instructions)." + Type: Diagnosis + Documentation: https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/ + Example: + id: pdc_head_and_mouth_example:case_147_diagnosis_0 + identifier: + - value: 107c25fa-4685-48e5-9f27-5d0316c67a4d + system: http://crdc.nci.nih.gov/gdc#diagnosis_id + subject: + id: pdc_head_and_mouth_example:case_147 + identifier: + - value: ff5a631f-93b9-486e-beb9-d16737db8c9e + system: http://crdc.nci.nih.gov/gdc#case_id + condition: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + tag: + - original + morphology: + coding: + - code: Not Reported + system: http://crdc.nci.nih.gov/gdc + related_specimen: + - id: pdc_head_and_mouth_example:case_147_sample_0 + identifier: + - value: bea8daca-7b9a-4aed-8448-747be0f898e2 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Solid Tissue Normal + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_147_sample_0_subject + identifier: + - value: ff5a631f-93b9-486e-beb9-d16737db8c9e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Normal + system: http://crdc.nci.nih.gov/gdc + - id: pdc_head_and_mouth_example:case_147_sample_1 + identifier: + - value: e4daf91c-b701-4e31-8922-7ca23fc0ea57 + system: http://crdc.nci.nih.gov/gdc + source_material_type: + coding: + - code: Primary Tumor + system: http://crdc.nci.nih.gov/gdc + source_subject: + id: pdc_head_and_mouth_example:case_147_sample_1_subject + identifier: + - value: ff5a631f-93b9-486e-beb9-d16737db8c9e + system: http://crdc.nci.nih.gov/gdc#case_id + general_tissue_pathology: + coding: + - code: Tumor + system: http://crdc.nci.nih.gov/gdc diff --git a/ccdh-pilot/test_transform_gdc.py b/ccdh-pilot/test_transform_gdc.py new file mode 100644 index 0000000..fb96ea2 --- /dev/null +++ b/ccdh-pilot/test_transform_gdc.py @@ -0,0 +1,342 @@ +#!/usr/bin/env python + +# +# test_transform_gdc.py - Import GDC data via public APIs and transform them into CRDC-H Instance data. +# + +import json +import yaml + +import crdch_model +import transform + +# Some general constants +EXAMPLE_PREFIX = "gdc_head_and_mouth_example:" +NCIT_URL = "http://ncithesaurus.nci.nih.gov" +CCDH_URL = "http://crdc.nci.nih.gov/ccdh" +GDC_URL = "http://crdc.nci.nih.gov/gdc" +ICD10_URL = "http://hl7.org/fhir/ValueSet/icd-10" + + +# Some codeable concepts we use repeatedly. +DAY = transform.codeable_concept(NCIT_URL, "C25301", "Day", tags=["harmonized"]) +MILLIGRAM = transform.codeable_concept( + NCIT_URL, "C28253", "Milligram", tags=["harmonized"] +) + + +# Convert a single GDC sample into a CRDC-H specimen. +def create_specimen( + gdc_sample, sample_index, gdc_diagnosis, diagnosis_index, gdc_case, case_index +): + specimen = crdch_model.Specimen( + id=f"{EXAMPLE_PREFIX}case_{case_index}_sample_{sample_index}", + ) + + if gdc_sample.get("sample_id"): + specimen.identifier = [ + crdch_model.Identifier(value=gdc_sample.get("sample_id"), system=GDC_URL) + ] + + if gdc_sample.get("submitter_id"): + submitter_identifier = crdch_model.Identifier( + value=gdc_sample.get("submitter_id"), system=GDC_URL + ) + if specimen.identifier: + specimen.identifier.append(submitter_identifier) + else: + specimen.identifier = [submitter_identifier] + + # TODO: figure out what to do about associated_project. + + # Make sure this is right. + if gdc_sample.get("submitter_id"): + specimen.source_subject = crdch_model.Subject( + id=f"{EXAMPLE_PREFIX}case_{case_index}_sample_{sample_index}_subject" + ) + specimen.source_subject.identifier = [ + crdch_model.Identifier( + value=gdc_sample.get("submitter_id"), system=f"{GDC_URL}#submitter_id" + ) + ] + + if gdc_case.get("case_id"): + case_id = crdch_model.Identifier( + value=gdc_case.get("case_id"), system=f"{GDC_URL}#case_id" + ) + if specimen.source_subject: + specimen.source_subject.identifier.append(case_id) + else: + specimen.source_subject = [case_id] + + # TODO: How do we calculate the Sample.type? + + if gdc_sample.get("sample_type"): + specimen.source_material_type = transform.codeable_concept( + GDC_URL, gdc_sample.get("sample_type") + ) + + # TODO: get the project_id somehow. + + if gdc_sample.get("tissue_type"): + specimen.general_tissue_pathology = transform.codeable_concept( + GDC_URL, gdc_sample.get("tissue_type") + ) + + if gdc_sample.get("tumor_code"): + specimen.specific_tissue_pathology = transform.codeable_concept( + GDC_URL, gdc_sample.get("tumor_code") + ) + + if gdc_sample.get("tumor_descriptor"): + specimen.tumor_status_at_collection = transform.codeable_concept( + GDC_URL, gdc_sample.get("tumor_descriptor") + ) + + if gdc_sample.get("current_weight"): + specimen.quantity_measure = crdch_model.SpecimenQuantityObservation( + observation_type=transform.codeable_concept( + NCIT_URL, "C25208", "Weight", tags=["harmonized"] + ), + value_quantity=transform.quantity_decimal( + gdc_sample.get("current_weight"), unit=MILLIGRAM + ), + ) + + # The following fields relate to the Specimen.creation_activity. + + if gdc_sample.get("days_to_collection"): + date_ended = crdch_model.TimePoint( + offset_from_index=transform.quantity_decimal( + gdc_sample.get("days_to_collection"), DAY + ), + index_time_point=crdch_model.TimePoint( + event_type=transform.codeable_concept( + NCIT_URL, "C142714", "Study Start", tags=["harmonized"] + ) + ), + ) + specimen.creation_activity = crdch_model.SpecimenCreationActivity( + date_ended=date_ended + ) + + if gdc_sample.get("initial_weight"): + initial_weight = transform.quantity_decimal( + gdc_sample.get("initial_weight"), MILLIGRAM + ) + if specimen.creation_activity: + specimen.creation_activity.quantity_collected = initial_weight + else: + specimen.creation_activity = crdch_model.SpecimenCreationActivity( + quantity_collected=initial_weight + ) + + if gdc_sample.get("biospecimen_anatomic_site"): + biospecimen_anatomic_site = transform.codeable_concept( + GDC_URL, + gdc_sample.get("biospecimen_anatomic_site"), + label=gdc_sample.get("biospecimen_anatomic_site"), + ) + if specimen.creation_activity: + specimen.creation_activity.collection_site = crdch_model.BodySite( + site=biospecimen_anatomic_site + ) + else: + specimen.creation_activity = crdch_model.SpecimenCreationActivity( + collection_site=crdch_model.BodySite(site=biospecimen_anatomic_site) + ) + + # if gdc_sample.get('time_between_excision_and_freezing'): + # time_obs = crdch_model.ExecutionTimeObservation( + # observation_type=transform.codeable_concept(CCDH_URL, 'time_between_excision_and_freezing', label='time_between_excision_and_freezing'), + # value_quantity=quantity(gdc_sample.get('time_between_excision_and_freezing'), DAY) + # ) + # if not specimen.creation_activity: + # specimen.creation_activity = crdch_model.SpecimenCreationActivity() + # if specimen.creation_activity.execution_time_observation: + # specimen.creation_activity.execution_time_observation.append(time_obs) + # else: + # specimen.creation_activity.execution_time_observation = [time_obs] + + # The following fields relate to the Specimen.processing_activity. + if gdc_sample.get("preservation_method"): + specimen.processing_activity = [ + crdch_model.SpecimenProcessingActivity( + activity_type=transform.codeable_concept( + GDC_URL, gdc_sample.get("preservation_method") + ) + ) + ] + + if gdc_sample.get("freezing_method"): + method_type = transform.codeable_concept( + GDC_URL, gdc_sample.get("freezing_method") + ) + if len(specimen.processing_activity) > 0: + specimen.processing_activity[0].method_type = method_type + else: + specimen.processing_activity = [ + crdch_model.SpecimenProcessingActivity(method_type=method_type) + ] + + return specimen + + +# Demonstrators +def test_transform_gdc_head_and_mouth(): + with open("head-and-mouth/gdc-head-and-mouth.json") as file: + gdc_head_and_mouth = json.load(file) + + # Each entry is a GDC case. To transform this into CRDC-H instance data, we need to + # transform it as a series of diagnoses. + diagnoses = [] + for (case_index, gdc_case) in enumerate(gdc_head_and_mouth): + for (diag_index, gdc_diagnosis) in enumerate(gdc_case["diagnoses"]): + diagnosis = crdch_model.Diagnosis( + id=f"{EXAMPLE_PREFIX}case_{case_index}_diagnosis_{diag_index}", + ) + + if gdc_diagnosis.get("diagnosis_id"): + diagnosis.identifier = [ + crdch_model.Identifier( + value=gdc_diagnosis["diagnosis_id"], + system=f"{GDC_URL}#diagnosis_id", + ) + ] + + diagnosis.subject = crdch_model.Subject( + id=f"{EXAMPLE_PREFIX}case_{case_index}" + ) + + if gdc_case.get("case_id"): + diagnosis.subject.identifier = [ + crdch_model.Identifier( + value=gdc_case.get("case_id"), system=f"{GDC_URL}#case_id" + ) + ] + + if gdc_case.get("submitter_id"): + diagnosis.subject.identifier.append( + crdch_model.Identifier( + value=gdc_case.get("submitter_id"), + system=f"{GDC_URL}#submitter_id", + ) + ) + + if gdc_diagnosis.get("age_at_diagnosis"): + diagnosis.age_at_diagnosis = transform.quantity_decimal( + gdc_diagnosis["age_at_diagnosis"], unit=DAY + ) + + if gdc_diagnosis.get("morphology"): + diagnosis.morphology = transform.codeable_concept( + GDC_URL, gdc_diagnosis.get("morphology") + ) + + condition_codings = [] + if gdc_diagnosis.get("primary_diagnosis"): + condition_codings.append( + crdch_model.Coding( + system=GDC_URL, + code=gdc_diagnosis.get("primary_diagnosis"), + tag=["original"], + ) + ) + + # TODO: double-check with DMH if this makes sense + if gdc_diagnosis.get("icd_10_code"): + condition_codings.append( + crdch_model.Coding( + system=ICD10_URL, + code=gdc_diagnosis.get("icd_10_code"), + tag=["original"], + ) + ) + + diagnosis.condition = crdch_model.CodeableConcept(coding=condition_codings) + + # TODO: PDC validation bug (in LinkML?) + # if gdc_diagnosis.get('tissue_or_organ_of_origin'): + # diagnosis.primary_site = crdch_model.BodySite( + # site=transform.codeable_concept(GDC_URL, gdc_diagnosis.get('tissue_or_organ_of_origin'), tags=['original']) + # ) + + if gdc_diagnosis.get("ajcc_staging_system_edition"): + observations = [] + + def add_observation(type_code, type_label, stage_code): + if stage_code: + observations.append( + crdch_model.CancerStageObservation( + observation_type=transform.codeable_concept( + GDC_URL, type_code, type_label, tags=["harmonized"] + ), + value_codeable_concept=transform.codeable_concept( + GDC_URL, stage_code, stage_code, tags=["original"] + ), + ) + ) + + # TODO: I couldn't find AJCC v7 in NCIt, so these codes reference the 8th edition. Need to be fixed. + # TODO: This is the first piece we should uncomment, because it triggers exactly the same error as when + # we try loading these observations from YAML. + # add_observation('C177555', 'AJCC v8 Clinical Stage', gdc_diagnosis.get('ajcc_clinical_stage')) + # add_observation('C177606', 'AJCC v8 Clinical M Category', gdc_diagnosis.get('ajcc_clinical_m')) + # add_observation('C177611', 'AJCC v8 Clinical N Category', gdc_diagnosis.get('ajcc_clinical_n')) + # add_observation('C177635', 'AJCC v8 Clinical T Category', gdc_diagnosis.get('ajcc_clinical_t')) + # add_observation('C177556', 'AJCC v8 Pathologic Stage', gdc_diagnosis.get('ajcc_pathologic_stage')) + # add_observation('C177607', 'AJCC v8 Pathologic M Category', gdc_diagnosis.get('ajcc_pathologic_m')) + # add_observation('C177612', 'AJCC v8 Pathologic N Category', gdc_diagnosis.get('ajcc_pathologic_n')) + # add_observation('C177636', 'AJCC v8 Pathologic T Category', gdc_diagnosis.get('ajcc_pathologic_t')) + + diagnosis.stage = [ + crdch_model.CancerStageObservationSet( + method_type=transform.codeable_concept( + GDC_URL, + gdc_diagnosis.get("ajcc_staging_system_edition"), + tags=["original"], + ), + observations=observations, + ) + ] + + # elif gdc_diagnosis.get('figo_stage'): + + # Year of diagnosis + if gdc_diagnosis.get("year_of_diagnosis"): + # TODO: We need to add support for approximate dates (https://github.com/cancerDHC/ccdhmodel/issues/130) + diagnosis.diagnosis_date = crdch_model.TimePoint() + diagnosis.diagnosis_date.date_time = ( + f"{gdc_diagnosis.get('year_of_diagnosis')}-01-01" + ) + + # Convert the specimen. + specimens = [ + create_specimen( + sample, sample_index, diagnosis, diag_index, gdc_case, case_index + ) + for (sample_index, sample) in enumerate(gdc_case.get("samples") or []) + ] + if len(specimens) > 0: + diagnosis.related_specimen = specimens + + # Write out the diagnosis. + diagnoses.append( + { + f"gdc_head_and_mouth_case_{case_index}_diagnosis_{diag_index}_diagnosis": { + "Provenance": "Downloaded from the GDC Public API (see " + + "https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb " + + 'for instructions)."', + "Type": "Diagnosis", + "Documentation": "https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/", + "Example": diagnosis, + } + } + ) + + # Write out all diagnoses into a single YAML file in the imported-node-data directory. + with open("ccdh-pilot/imported-node-data/gdc-head-and-mouth.yaml", "w") as f: + yaml.dump_all(diagnoses, f, Dumper=yaml.SafeDumper, sort_keys=False) + + # yaml.dump(linkml_runtime.utils.formatutils.remove_empty_items(element, hide_protected_keys=True), + # Dumper=yaml.SafeDumper, sort_keys=False, diff --git a/ccdh-pilot/test_transform_pdc.py b/ccdh-pilot/test_transform_pdc.py new file mode 100644 index 0000000..be7725d --- /dev/null +++ b/ccdh-pilot/test_transform_pdc.py @@ -0,0 +1,347 @@ +#!/usr/bin/env python + +# +# test_transform_pdc.py - Import PDC data via public APIs and transform them into CRDC-H Instance data. +# + +import json +import yaml + +import crdch_model +import transform + +# Some general constants +EXAMPLE_PREFIX = "pdc_head_and_mouth_example:" +NCIT_URL = "http://ncithesaurus.nci.nih.gov" +CCDH_URL = "http://crdc.nci.nih.gov/ccdh" +GDC_URL = "http://crdc.nci.nih.gov/gdc" +ICD10_URL = "http://hl7.org/fhir/ValueSet/icd-10" + + +# Some codeable concepts we use repeatedly. +DAY = transform.codeable_concept(NCIT_URL, "C25301", "Day", tags=["harmonized"]) +MILLIGRAM = transform.codeable_concept( + NCIT_URL, "C28253", "Milligram", tags=["harmonized"] +) + + +# Convert a single PDC sample into a CRDC-H specimen. +def create_specimen( + gdc_sample, sample_index, gdc_diagnosis, diagnosis_index, gdc_case, case_index +): + specimen = crdch_model.Specimen( + id=f"{EXAMPLE_PREFIX}case_{case_index}_sample_{sample_index}", + ) + + if gdc_sample.get("sample_id"): + specimen.identifier = [ + crdch_model.Identifier(value=gdc_sample.get("sample_id"), system=GDC_URL) + ] + + if gdc_sample.get("submitter_id"): + submitter_identifier = crdch_model.Identifier( + value=gdc_sample.get("submitter_id"), system=GDC_URL + ) + if specimen.identifier: + specimen.identifier.append(submitter_identifier) + else: + specimen.identifier = [submitter_identifier] + + # TODO: figure out what to do about associated_project. + + # Make sure this is right. + if gdc_sample.get("submitter_id"): + specimen.source_subject = crdch_model.Subject( + id=f"{EXAMPLE_PREFIX}case_{case_index}_sample_{sample_index}_subject" + ) + specimen.source_subject.identifier = [ + crdch_model.Identifier( + value=gdc_sample.get("submitter_id"), system=f"{GDC_URL}#submitter_id" + ) + ] + + if gdc_case.get("case_id"): + case_id = crdch_model.Identifier( + value=gdc_case.get("case_id"), system=f"{GDC_URL}#case_id" + ) + if not specimen.source_subject: + specimen.source_subject = crdch_model.Subject( + id=f"{EXAMPLE_PREFIX}case_{case_index}_sample_{sample_index}_subject" + ) + + if specimen.source_subject.identifier: + specimen.source_subject.identifier.append(case_id) + else: + specimen.source_subject.identifier = [case_id] + + # TODO: How do we calculate the Sample.type? + + if gdc_sample.get("sample_type"): + specimen.source_material_type = transform.codeable_concept( + GDC_URL, gdc_sample.get("sample_type") + ) + + # TODO: get the project_id somehow. + + if gdc_sample.get("tissue_type"): + specimen.general_tissue_pathology = transform.codeable_concept( + GDC_URL, gdc_sample.get("tissue_type") + ) + + if gdc_sample.get("tumor_code"): + specimen.specific_tissue_pathology = transform.codeable_concept( + GDC_URL, gdc_sample.get("tumor_code") + ) + + if gdc_sample.get("tumor_descriptor"): + specimen.tumor_status_at_collection = transform.codeable_concept( + GDC_URL, gdc_sample.get("tumor_descriptor") + ) + + if gdc_sample.get("current_weight"): + specimen.quantity_measure = crdch_model.SpecimenQuantityObservation( + observation_type=transform.codeable_concept( + NCIT_URL, "C25208", "Weight", tags=["harmonized"] + ), + value_quantity=transform.quantity_decimal( + gdc_sample.get("current_weight"), unit=MILLIGRAM + ), + ) + + # The following fields relate to the Specimen.creation_activity. + + if gdc_sample.get("days_to_collection"): + date_ended = crdch_model.TimePoint( + offset_from_index=transform.quantity_decimal( + gdc_sample.get("days_to_collection"), DAY + ), + index_time_point=crdch_model.TimePoint( + event_type=transform.codeable_concept( + NCIT_URL, "C142714", "Study Start", tags=["harmonized"] + ) + ), + ) + specimen.creation_activity = crdch_model.SpecimenCreationActivity( + date_ended=date_ended + ) + + if gdc_sample.get("initial_weight"): + initial_weight = transform.quantity_decimal( + gdc_sample.get("initial_weight"), MILLIGRAM + ) + if specimen.creation_activity: + specimen.creation_activity.quantity_collected = initial_weight + else: + specimen.creation_activity = crdch_model.SpecimenCreationActivity( + quantity_collected=initial_weight + ) + + if gdc_sample.get("biospecimen_anatomic_site"): + biospecimen_anatomic_site = transform.codeable_concept( + GDC_URL, + gdc_sample.get("biospecimen_anatomic_site"), + label=gdc_sample.get("biospecimen_anatomic_site"), + ) + if specimen.creation_activity: + specimen.creation_activity.collection_site = crdch_model.BodySite( + site=biospecimen_anatomic_site + ) + else: + specimen.creation_activity = crdch_model.SpecimenCreationActivity( + collection_site=crdch_model.BodySite(site=biospecimen_anatomic_site) + ) + + # if gdc_sample.get('time_between_excision_and_freezing'): + # time_obs = crdch_model.ExecutionTimeObservation( + # observation_type=transform.codeable_concept(CCDH_URL, 'time_between_excision_and_freezing', label='time_between_excision_and_freezing'), + # value_quantity=quantity(gdc_sample.get('time_between_excision_and_freezing'), DAY) + # ) + # if not specimen.creation_activity: + # specimen.creation_activity = crdch_model.SpecimenCreationActivity() + # if specimen.creation_activity.execution_time_observation: + # specimen.creation_activity.execution_time_observation.append(time_obs) + # else: + # specimen.creation_activity.execution_time_observation = [time_obs] + + # The following fields relate to the Specimen.processing_activity. + if gdc_sample.get("preservation_method"): + specimen.processing_activity = [ + crdch_model.SpecimenProcessingActivity( + activity_type=transform.codeable_concept( + GDC_URL, gdc_sample.get("preservation_method") + ) + ) + ] + + if gdc_sample.get("freezing_method"): + method_type = transform.codeable_concept( + GDC_URL, gdc_sample.get("freezing_method") + ) + if len(specimen.processing_activity) > 0: + specimen.processing_activity[0].method_type = method_type + else: + specimen.processing_activity = [ + crdch_model.SpecimenProcessingActivity(method_type=method_type) + ] + + return specimen + + +# Demonstrators +def test_transform_pdc_head_and_mouth(): + with open("head-and-mouth/pdc-head-and-mouth.json") as file: + pdc_head_and_mouth = json.load(file) + + # Each entry is a PDC case. To transform this into CRDC-H instance data, we need to + # transform it as a series of diagnoses. + diagnoses = [] + for (case_index, gdc_case) in enumerate(pdc_head_and_mouth): + for (diag_index, gdc_diagnosis) in enumerate(gdc_case["diagnoses"]): + diagnosis = crdch_model.Diagnosis( + id=f"{EXAMPLE_PREFIX}case_{case_index}_diagnosis_{diag_index}", + ) + + if gdc_diagnosis.get("diagnosis_id"): + diagnosis.identifier = [ + crdch_model.Identifier( + value=gdc_diagnosis["diagnosis_id"], + system=f"{GDC_URL}#diagnosis_id", + ) + ] + + diagnosis.subject = crdch_model.Subject( + id=f"{EXAMPLE_PREFIX}case_{case_index}" + ) + + if gdc_case.get("case_id"): + diagnosis.subject.identifier = [ + crdch_model.Identifier( + value=gdc_case.get("case_id"), system=f"{GDC_URL}#case_id" + ) + ] + + if gdc_case.get("submitter_id"): + diagnosis.subject.identifier.append( + crdch_model.Identifier( + value=gdc_case.get("submitter_id"), + system=f"{GDC_URL}#submitter_id", + ) + ) + + if gdc_diagnosis.get("age_at_diagnosis"): + diagnosis.age_at_diagnosis = transform.quantity_decimal( + gdc_diagnosis["age_at_diagnosis"], DAY + ) + + if gdc_diagnosis.get("morphology"): + diagnosis.morphology = transform.codeable_concept( + GDC_URL, gdc_diagnosis.get("morphology") + ) + + condition_codings = [] + if gdc_diagnosis.get("primary_diagnosis"): + condition_codings.append( + crdch_model.Coding( + system=GDC_URL, + code=gdc_diagnosis.get("primary_diagnosis"), + tag=["original"], + ) + ) + + # TODO: double-check with DMH if this makes sense + if gdc_diagnosis.get("icd_10_code"): + condition_codings.append( + crdch_model.Coding( + system=ICD10_URL, + code=gdc_diagnosis.get("icd_10_code"), + tag=["original"], + ) + ) + + diagnosis.condition = crdch_model.CodeableConcept(coding=condition_codings) + + # TODO: PDC validation bug (in LinkML?) + # if gdc_diagnosis.get('tissue_or_organ_of_origin'): + # diagnosis.primary_site = crdch_model.BodySite( + # site=codeable_concept(GDC_URL, gdc_diagnosis.get('tissue_or_organ_of_origin'), tags=['original']) + # ) + + if gdc_diagnosis.get("ajcc_staging_system_edition"): + observations = [] + + def add_observation(type_code, type_label, stage_code): + if stage_code: + observations.append( + crdch_model.CancerStageObservation( + observation_type=transform.codeable_concept( + GDC_URL, type_code, type_label, tags=["harmonized"] + ), + value_codeable_concept=transform.codeable_concept( + GDC_URL, stage_code, stage_code, tags=["original"] + ), + ) + ) + + # TODO: I couldn't find AJCC v7 in NCIt, so these codes reference the 8th edition. Need to be fixed. + # TODO: This is the first piece we should uncomment, because it triggers exactly the same error as when + # we try loading these observations from YAML. + # add_observation('C177555', 'AJCC v8 Clinical Stage', gdc_diagnosis.get('ajcc_clinical_stage')) + # add_observation('C177606', 'AJCC v8 Clinical M Category', gdc_diagnosis.get('ajcc_clinical_m')) + # add_observation('C177611', 'AJCC v8 Clinical N Category', gdc_diagnosis.get('ajcc_clinical_n')) + # add_observation('C177635', 'AJCC v8 Clinical T Category', gdc_diagnosis.get('ajcc_clinical_t')) + # add_observation('C177556', 'AJCC v8 Pathologic Stage', gdc_diagnosis.get('ajcc_pathologic_stage')) + # add_observation('C177607', 'AJCC v8 Pathologic M Category', gdc_diagnosis.get('ajcc_pathologic_m')) + # add_observation('C177612', 'AJCC v8 Pathologic N Category', gdc_diagnosis.get('ajcc_pathologic_n')) + # add_observation('C177636', 'AJCC v8 Pathologic T Category', gdc_diagnosis.get('ajcc_pathologic_t')) + + diagnosis.stage = [ + crdch_model.CancerStageObservationSet( + method_type=transform.codeable_concept( + GDC_URL, + gdc_diagnosis.get("ajcc_staging_system_edition"), + tags=["original"], + ), + observations=observations, + ) + ] + + # elif gdc_diagnosis.get('figo_stage'): + + # Year of diagnosis + if gdc_diagnosis.get("year_of_diagnosis"): + # TODO: We need to add support for approximate dates (https://github.com/cancerDHC/ccdhmodel/issues/130) + diagnosis.diagnosis_date = crdch_model.TimePoint() + diagnosis.diagnosis_date.date_time = ( + f"{gdc_diagnosis.get('year_of_diagnosis')}-01-01" + ) + + # Convert the specimen. + specimens = [ + create_specimen( + sample, sample_index, diagnosis, diag_index, gdc_case, case_index + ) + for (sample_index, sample) in enumerate(gdc_case.get("samples") or []) + ] + if len(specimens) > 0: + diagnosis.related_specimen = specimens + + # Write out the diagnosis. + diagnoses.append( + { + f"pdc_head_and_mouth_example_{case_index}_diagnosis_{diag_index}_diagnosis": { + "Provenance": "Downloaded from the GDC Public API (see " + + "https://github.com/cancerDHC/example-data/blob/main/head-and-mouth/Head%20and%20Mouth%20Cancer%20Datasets.ipynb " + + 'for instructions)."', + "Type": "Diagnosis", + "Documentation": "https://cancerdhc.github.io/ccdhmodel/v1.1/Diagnosis/", + "Example": diagnosis, + } + } + ) + + # Write out all diagnoses into a single YAML file in the imported-node-data directory. + with open("ccdh-pilot/imported-node-data/pdc-head-and-mouth.yaml", "w") as f: + yaml.dump_all(diagnoses, f, Dumper=yaml.SafeDumper, sort_keys=False) + + # yaml.dump(linkml_runtime.utils.formatutils.remove_empty_items(element, hide_protected_keys=True), + # Dumper=yaml.SafeDumper, sort_keys=False, diff --git a/ccdh-pilot/test_validate_all.py b/ccdh-pilot/test_validate_all.py new file mode 100644 index 0000000..4026146 --- /dev/null +++ b/ccdh-pilot/test_validate_all.py @@ -0,0 +1,101 @@ +import glob +import logging +import os + +import crdch_model +import jsonschema +import requests +import yaml +from linkml_runtime.loaders.yaml_loader import YAMLLoader + + +# Generate tests for each file to validate. +def pytest_generate_tests(metafunc): + # Identify all the files that need to be validated. + # These are all the YAML files in this directory or any subdirectories. + path_to_script = os.path.dirname(os.path.abspath(__file__)) + query = os.path.join(path_to_script, "**", "*.yaml") + files_to_validate = glob.glob(query, recursive=True) + + metafunc.parametrize("input_file", files_to_validate) + + +# Test each input file. +def test_files(input_file): + # JSON Schema URL + json_schema_url = "https://raw.githubusercontent.com/cancerDHC/ccdhmodel/main/crdch_model/json_schema/crdch_model.schema.json" + req = requests.get(json_schema_url) + ccdh_json_schema = req.json() + + # We need a RefResolver for the entire schema. + ref_resolver = jsonschema.RefResolver.from_schema(ccdh_json_schema) + + # TODO: change this to relative paths + with open(input_file) as f: + logging.info(f"Validating {input_file}") + examples = yaml.load_all(f, Loader=yaml.FullLoader) + + for entry in examples: + first_key = list(entry)[0] + example = entry[first_key]["Example"] + if first_key.endswith("_specimen"): + specimen = YAMLLoader().load(example, crdch_model.Specimen) + validator = jsonschema.Draft7Validator( + ccdh_json_schema["$defs"]["Specimen"], ref_resolver + ) + errors = validator.iter_errors(example) + for error in errors: + logging.error( + f"Validation error in {input_file} at {error.path}: {error.message}" + ) + validator.validate(example) + elif first_key.endswith("_subject"): + subject = YAMLLoader().load(example, crdch_model.Subject) + validator = jsonschema.Draft7Validator( + ccdh_json_schema["$defs"]["Subject"], ref_resolver + ) + errors = validator.iter_errors(example) + for error in errors: + logging.error( + f"Validation error in {input_file} at {error.path}: {error.message}" + ) + validator.validate(example) + elif first_key.endswith("_research_project"): + research_project = YAMLLoader().load( + example, crdch_model.ResearchProject + ) + validator = jsonschema.Draft7Validator( + ccdh_json_schema["$defs"]["ResearchProject"], ref_resolver + ) + errors = validator.iter_errors(example) + for error in errors: + logging.error( + f"Validation error in {input_file} at {error.path}: {error.message}" + ) + validator.validate(example) + elif first_key.endswith("_research_subject"): + research_subject = YAMLLoader().load( + example, crdch_model.ResearchSubject + ) + validator = jsonschema.Draft7Validator( + ccdh_json_schema["$defs"]["ResearchSubject"], ref_resolver + ) + errors = validator.iter_errors(example) + for error in errors: + logging.error( + f"Validation error in {input_file} at {error.path}: {error.message}" + ) + validator.validate(example) + elif first_key.endswith("_diagnosis"): + diagnosis = YAMLLoader().load(example, crdch_model.Diagnosis) + validator = jsonschema.Draft7Validator( + ccdh_json_schema["$defs"]["Diagnosis"], ref_resolver + ) + errors = validator.iter_errors(example) + for error in errors: + logging.error( + f"Validation error in {input_file} at {error.path}: {error.message}" + ) + validator.validate(example) + else: + raise RuntimeError(f"Could not load entry: {entry}") diff --git a/ccdh-pilot/transform.py b/ccdh-pilot/transform.py new file mode 100644 index 0000000..72a3c89 --- /dev/null +++ b/ccdh-pilot/transform.py @@ -0,0 +1,29 @@ +# Shared code for transforming data into the CRDC-H instance format. +# The goal is to eventually build a library that we can move into the ccdhmodel repo +# as a part of the crdch_model repository, implementing what is effectively a +# domain-specific language for doing transforms into the CRDC-H instance format. + +import crdch_model + + +def codeable_concept(system, code, label=None, text=None, tags=[]): + """Create a crdch_model.CodeableConcept for a given [single] system and code.""" + coding = crdch_model.Coding(system=system, code=code) + if label is not None: + coding.label = label + if len(tags) > 0: + coding.tag = tags + cc = crdch_model.CodeableConcept(coding) + if text is not None: + cc.text = text + return cc + + +def quantity_decimal(value_decimal, unit): + """Create a crdch_model.Quantity for a given decimal value and a unit (expressed as a CodeableConcept).""" + q = crdch_model.Quantity(unit=unit) + # TODO: this should be converted to a Decimal, but that doesn't work/pass validation + # So instead we truncate it to an integer for now. + # Filed as issue https://github.com/cancerDHC/ccdhmodel/issues/131 + q.value_decimal = int(value_decimal) + return q diff --git a/head-and-mouth/diagnoses.jsonld b/head-and-mouth/diagnoses.jsonld index ebaef75..135383a 100644 --- a/head-and-mouth/diagnoses.jsonld +++ b/head-and-mouth/diagnoses.jsonld @@ -91547,7 +91547,7 @@ } ], "@context": { - "_comments": "Auto generated from crdch_model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-11-18T18:29:32\n Schema: CRDC-H\n \n id: https://example.org/crdch\n description: \n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", + "_comments": "Auto generated from crdch_model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2022-01-05T17:16:30\n Schema: CRDC-H\n \n id: https://example.org/crdch\n description: \n license: https://creativecommons.org/publicdomain/zero/1.0/\n ", "@context": { "GDC": "http://example.org/gdc/", "HTAN": "http://example.org/htan/", diff --git a/head-and-mouth/diagnoses.ttl b/head-and-mouth/diagnoses.ttl index 7b2d716..4dd28fd 100644 --- a/head-and-mouth/diagnoses.ttl +++ b/head-and-mouth/diagnoses.ttl @@ -4,63 +4,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e7f08842-7c61-469c-829a-feff82339bee" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008328-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "6d1a6236-3625-4300-9f12-4e666cb2694a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "40d016b6-27a3-4e33-ad6b-f50eaa54e2fa" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008097-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f71f4733-17f4-436f-b12d-bad5b99ceba3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d20b4711-8757-5d39-a8cc-b8ece86592cd" ; + crdch:id "87e9b232-8b59-573b-9758-c7b5456d6fc0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7430_diagnosis" ] ; + crdch:value "TCGA-CV-7248_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -70,187 +16,155 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6bd53676-487f-4661-8e01-739b3b856cee" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "5fe254fc-76cd-4081-a46f-574f2ec76d10" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0e0af838-3a62-44a6-9e8e-0f9ba07730fa" ; + crdch:id "24a2dd45-0453-4bfa-af4c-cde8cb0c0cfb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c22e9fe0-a052-4c6f-9fb2-e58289277e2a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "da9132d5-4a55-4d7a-bb7f-7990af380dcb" ; + crdch:id "791203c3-4192-4844-b32a-0f21944333e1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e5ab53bf-073a-49e7-9402-8e7261d385c8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; + crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c7db86f3-b6c1-59db-961c-534b91393b19" ; + crdch:id "c58ca3ba-23a8-472b-aab3-94382be12940" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6010_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-010867-8727_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "cece12a4-5f68-4a6d-8815-e88495da08f4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "904e12f8-ab59-4ad8-8096-7b82f9388d70" ; + crdch:id "d492bfd2-b37d-49c3-a8d5-40171e8442d5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "60a003d8-42fa-4981-8fa8-a96a6f4205ad" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0019316-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:43:52.092583-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cd2a5d45-9bae-4c96-b8dd-7ad079153a49" ; + crdch:id "b3eb534b-6441-4294-809a-ab6963d9aa39" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c0bc6849-2b35-4465-9d65-38c3a21a9a25" ; + crdch:id "ea9b7e18-cbc5-4588-8b59-d32af85db2c0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0019226-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-DFCI-052774-173461_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:42:00.849990-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:20:30.865187-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b33d58a0-8855-42ac-baaa-0a1e961307f4" ; + crdch:id "f37609a0-84b8-4203-9497-9f60cc8be539" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -264,67 +178,59 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5d8267c6-4156-5145-b6e3-49c68f8cabfb" ; + crdch:id "2edff908-b791-5c44-b0ed-cdbad3c1a249" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5361_diagnosis" ] ; + crdch:value "TCGA-CV-7418_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "26eac019-6e9b-4ab1-aa1b-323f76d9aef3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2877214f-4aab-46cf-b052-b6e7d2662ff5" ; + crdch:id "ccd7a7be-3065-4f30-8d21-94bfdc0b4703" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5b2581d8-c087-4caa-b9ce-bc0168fbfefa" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "2e5b2590-4227-4265-a837-8175920e4d01" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c807171a-4433-4246-a454-c5cf768da8aa" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "cc37f4d1-d8ae-4367-8abf-7c6da579d09e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; @@ -336,87 +242,51 @@ crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f9a0b1dd-a13b-4a14-ac22-c9570e02ca60" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008792-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b882dbe8-5494-4092-8bad-ccca6b119775" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "43aa2337-12ee-410b-9182-0de9352057f0" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD3230_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:59:56.723939-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "900eabba-ab2e-4b0b-9738-db52f9203db9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d2b0be44-b12f-443f-9d48-3e26ea1ed386" ; + crdch:id "e7f08842-7c61-469c-829a-feff82339bee" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD7867_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0008328-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:48:10.807261-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1fc039e3-94d1-4fe2-9d51-796dce543f9f" ; + crdch:id "6d1a6236-3625-4300-9f12-4e666cb2694a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -425,151 +295,91 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "ce0e772c-45e6-4686-9db5-f88e05e2f713" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f6106a03-d94d-5b31-969b-ddd1d6ac23f7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD12118_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-BB-8596_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:00:58.377064-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fb315485-9a4d-42a8-8e1b-8cc97c708f1d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "6759d804-a7db-43ed-a3ae-db633fdc7cdb" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010241-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:id "226992b4-f81f-49f5-a1da-37ab1742779b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "856fab11-14d9-4e8c-af8a-65684ca39418" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "bddca644-5ced-5789-8d31-c00df9f776ad" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-A74Q_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; - crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c03b3dfa-7b9b-4a21-9274-d174bc14440b" ; + crdch:id "b8077f12-81e6-49f1-aa69-a4b6f5825534" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "343c1ea3-2785-465f-b01a-2d609b486ef9" ; + crdch:id "51eeba12-4cfb-4842-ad6c-e49cfe5ef207" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d9095c8b-414f-41d4-a478-ee54d2728762" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ] ] . @@ -577,72 +387,41 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "40954a8e-e4c2-5604-937b-0a79ac7489d2" ; + crdch:id "4e06969c-5592-59ad-b006-09cb82ce6cc9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7261_diagnosis" ] ; + crdch:value "TCGA-D6-6517_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "a7692585-a129-4671-bfe5-98342a326776" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b069c55b-496a-4a57-a507-1b2e1b4201ae" ; + crdch:id "53450297-c715-4c54-ad7e-3152a1e16c45" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "00f7bc3c-c0e7-42bf-84d7-87a8a539bd4a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "a2dd87a8-e0d1-47c1-a8d1-70b9730aa4ba" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "69a89590-eb61-41d5-b33e-e7bc5adb92bf" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "8c099f45-3fd6-4966-8cdb-ca4b9288b1a2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; @@ -654,131 +433,93 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "cecde3bd-c011-5cd9-8071-912a0f342eb8" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A7JJ_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; - crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "de8517e0-d7ad-41a2-9468-bdf0106c905c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "392cbac9-ed5a-4f0c-9270-f45278476c73" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "408c2c68-2f92-421e-b797-ecada0bfedc7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "stage iii" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; + crdch:system "GDC" ] ; + crdch:text "Malignant rhabdoid tumor" ] ; + crdch:id "9a11a042-337d-5a91-b483-093f98b0b72f" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TARGET-52-PARKKN_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:system "GDC" ] ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:system "GDC" ] ; + crdch:text "8963/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ced7edc7-a9ff-5d30-a63d-dbed4edfe497" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "unknown" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c8d65c8c-9299-49bc-bfe0-97c19ff35fd2" ; + crdch:id "c34f7850-ab91-4173-b716-b487c290ec78" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037050-88705_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0012862-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "58a5858d-4740-4da1-8959-43d7b05ae1ea" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "59d43c02-f731-4a7f-97ae-c3d7dac2d5e0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -789,52 +530,77 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "8b48f2a0-f69b-547c-a9df-35b18ec7bb5a" ; + crdch:id "fc929f30-0322-43c4-b12f-ddff9d8a2335" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A63U_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-010590-8636_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b4430e0f-983c-454d-926e-a33fcb4cd02c" ; + crdch:id "175e9244-58cb-4b1a-9614-a4fb1c0e6603" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "dd691506-83cb-50c1-ae0a-2583d57079d3" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CN-A499_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:system "GDC" ] ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a6af965f-ae37-421d-98d6-a69ce62213ac" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "9ca906ce-18f9-41c5-afcc-353b26fdebaa" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "812b8ee1-096a-40ff-914d-9957644b7d11" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "7d93ba42-9e87-4a6c-8b0d-6f185645a90a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -844,132 +610,94 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "MX" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "becd7cb0-9352-5c38-856c-fcfa539fdea3" ; + crdch:id "f0cdd17d-5db9-4c58-84f5-f9efcc94dcb5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5431_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0004492-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "39e3facf-6d13-4611-bcfa-90ef0350814d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "d74d27e4-88e8-4ce3-a1ff-7658e007a49a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "be567c0a-3833-45d7-b846-d229a8e16e16" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "3c0d1fbc-508c-4cad-a9eb-a848fc20ac76" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-006868-2957_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8897e2b3-1863-43c7-a84f-fe53d12371f9" ; + crdch:id "abf5cf5e-2352-4ba7-9a91-cbefe78ae28e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "af6475d1-2529-4772-9e9e-ce83e3dc0cf8" ; + crdch:id "ad342355-cfa9-458f-8723-7a099368b797" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008645-7086_diagnosis" ] ; + crdch:value "GENIE-DFCI-008794-7198_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; @@ -980,7 +708,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "30b0ff9c-3106-4ce0-8657-3ed59c1c8fc7" ; + crdch:id "536ca98b-7415-49d8-84c2-dca4b5070ff6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -994,20 +722,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "65bd5ce4-bf44-4994-824e-f21701449f73" ; + crdch:id "fd3fbe29-2fa3-41f7-99c9-51d3d05ff5b4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-NKI-HMII-Q9EY_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-DFCI-003147-99_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cb629447-dbb7-49c7-a88a-435b6b6decda" ; + crdch:id "13654c9a-afcc-4635-9885-8418a318ac7a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -1018,29 +746,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "552900c2-144c-4340-aed9-197382fafed4" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "64ba1bbd-bf72-4700-97be-0bc054876c84" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD17916_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-005062-1372_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:57:41.511744-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d4c804df-7392-4267-908e-8fe8c37d00cd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "a0deb101-019f-46d7-8cb2-ee98c9d7aa92" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -1051,112 +776,131 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "afec3d92-5a3c-5b04-a2f1-49031942cc1d" ; + crdch:id "58498007-02e8-41fb-b884-2383b5eb1414" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A6IH_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "GENIE-DFCI-007582-3990_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "63b4690f-f247-4874-9923-e96375c56a01" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:44:49.261364-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5f210369-1839-4f18-b081-974efc7de032" ; + crdch:id "f198873e-fb8b-4ddb-8d79-1fcf1bb1d764" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "9c1cd7ed-46f5-4809-a898-22cc0e15cd64" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-438c3609-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0d0194eb-d83f-4028-9b4b-3308c0207133" ; + crdch:id "bc168208-ee4f-4a50-8ddf-b72b0dd59da2" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4b" ; - crdch:system "GDC" ] ; - crdch:text "T4b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "09912911-2865-490c-aaca-89f4cc1bee36" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-008390-5815_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7894955b-ac0e-46ee-a5b3-c023cd1e87b6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Adenocarcinoma, NOS" ] ; + crdch:id "25182ec3-0d7b-44ca-82e4-f1a8d7de4a28" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD18004_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; + crdch:system "GDC" ] ; + crdch:text "8140/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:58:46.365657-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b62fca52-48c3-4bea-b5f7-5794a1ed4f43" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d4b595ef-5e2f-4722-bf4e-48bb831bc057" ; + crdch:id "2ba98ec4-5cc5-43d5-8de3-ab33d0d6779b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-002065-124_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-DFCI-003996-1286_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "172019a6-18cf-4532-89ec-9f4ec83dee30" ; + crdch:id "12d6861e-5ad9-48f7-ae61-07c7e45be5a3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -1167,115 +911,136 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "cdd012e7-6539-5ffe-a4b7-b36a6233b1ec" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "1b2f7aa9-bc17-4cfa-8d93-b5a7bdd68bfe" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A6DJ_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "GENIE-MSK-P-0015451-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "735334b4-6c30-4a7a-aa54-63f506b8e2bb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "8a18a085-a8a0-4fd0-9468-33e10fe1c55d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "86e71958-485e-53c6-831a-c456ec617b7b" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-HD-7229_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4210ffee-2a83-4f05-8935-2687503c83d4" ; + crdch:id "9fbf3123-c654-4f2c-b41a-ac4dc029a5d9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f1367475-a5f1-4a0f-aa73-5a703a3accaf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bbee89dc-6858-45c3-a9fc-c455851f96a8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "1169973a-8575-4d2b-8da8-36a83aa5f947" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; - crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6dd63ec3-e88a-4da9-be07-0d11a1768dbf" ; + crdch:id "6cba02c0-48e0-4424-964c-a104a6652d07" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0004416-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-007903-6035_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "34487c7a-5f9a-41b0-8ced-d7c2ce3653e2" ; + crdch:id "fbd21489-29cd-4d9b-8d7c-e04342040edc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -1289,9 +1054,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bd3c4df6-90f0-58df-8713-51ca36d74124" ; + crdch:id "d20b4711-8757-5d39-a8cc-b8ece86592cd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A6V3_diagnosis" ] ; + crdch:value "TCGA-CV-7430_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -1301,95 +1066,104 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "285e2354-8efd-4951-87cf-0e188d11423e" ; + crdch:id "6bd53676-487f-4661-8e01-739b3b856cee" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "c22e9fe0-a052-4c6f-9fb2-e58289277e2a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "da9132d5-4a55-4d7a-bb7f-7990af380dcb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "97657453-6a97-4879-9440-fd0eea9d5f33" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "0e0af838-3a62-44a6-9e8e-0f9ba07730fa" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "45950ba0-9179-4304-9bf7-1a43880d000b" ; + crdch:id "494e7724-f0c8-44b8-a4f9-8e6cc9a2c095" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010940-9514_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-NKI-FGHG-R6TZ_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8642c059-a648-4ced-977f-45d6e6496e7b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "e91ef1f0-a986-44d2-8880-fbef0afe91d8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Not Reported" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -1400,116 +1174,137 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cceca036-354c-59e4-ad7a-886865aada46" ; + crdch:id "18cabf3d-233d-5ad2-a5d3-a2a10677c99a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7245_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-BA-A4II_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f0684e03-2d91-4e9b-9d11-a3063ccc2f34" ; + crdch:id "81bbc439-0c8c-4d39-bef2-03901b31c50e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d455327a-a947-4a67-8fb5-44438abe5976" ; + crdch:id "a76bfc3e-fa46-4a65-88e7-c644c8b20098" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "aaa6607c-e333-4f99-b1dc-390c3cad4f1b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c8ac9749-82ff-4348-8d91-5ce677697a15" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "Stage I" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0e732992-a174-4861-8e05-a6c3e21107b3" ; + crdch:id "5cb1278d-4b33-401c-b200-b4408788c927" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001903-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-DFCI-002669-7683_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ea373411-6d3c-4ee3-b8c1-d79131847aa1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "4d69eeb9-81bd-4146-9a4a-3ca86c789272" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "bbbf3549-d0cf-4dcc-bc92-32d12cd2c96b" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD10083_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:54:12.244834-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "712ad6f8-8c2a-4c82-a89a-10ff849e3e9e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -1520,20 +1315,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "155a3146-d68b-4058-abe2-3ae8713641ce" ; + crdch:id "2326f9b7-e2e8-487a-acd4-b00bc9967a8e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-5361-16435_diagnosis" ] ; + crdch:value "GENIE-MDA-6597-17790_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a7b07575-200a-4a32-8faa-075ded8667cc" ; + crdch:id "35f0c152-0c87-42bb-a1b7-b306e66514f5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -1547,123 +1342,145 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1fdbf271-8b0c-5d7b-bacf-d883e0d0d054" ; + crdch:id "4943c82a-30d2-4c85-a233-032a49ca801d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5360_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-008342-5809_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0c00768e-8b13-4b8e-80fc-b344740845f1" ; + crdch:id "e01da120-9c9d-4ef7-8568-525f74222dd5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "9439bc03-9d26-454a-ba80-a0f5a4585656" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "c508644c-d496-4647-a065-4e0077d99b67" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-008357-5599_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "740cef36-1319-4096-8ba3-8e6fce6282da" ; + crdch:id "80c31730-c365-4f43-ae30-d082f4c7f67a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "5fddab5d-aebe-4b6a-9812-a6edc05c51cc" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-008897-6910_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f8a73605-d802-4364-aa6e-5d23691f92cf" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "0f72e73b-f462-4eef-9d1e-95e83c1f2aaf" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD5362_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:05.012118-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "9f4929bc-09a7-47b8-9720-d6f829b51a13" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "022d6f9b-38da-5bfb-8bd9-e800361481a0" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "7ed3e77f-cc81-56cb-b573-cc6df309ff48" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-A6EK_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-BB-4227_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0a64b28d-8dde-4eaf-bac5-217406cbc4c6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "f31d010d-cb3e-46da-9647-38fdb9d1bbc0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ad47c17b-e21c-4aed-aac6-8a062c6b5e42" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "a6748675-5433-4f39-a578-9a1ddb8bb1b3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b3a55bcd-1f88-4d25-9f95-5ef7393d6cf0" ; + crdch:id "0e81b0ef-6f16-4a56-9f18-8acad8bf9ccf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -1673,75 +1490,69 @@ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ada2a9ee-43ec-4198-b1e4-bb0c62102973" ; + crdch:id "d5b740be-4c9a-4bec-835a-4cd0b394ded4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003061-9096_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-006383-3525_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7d368af5-dc58-4ddb-af35-cbc63bd638e4" ; + crdch:id "1a1294ab-79bf-4e29-b958-cd6c3b25a984" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -1755,20 +1566,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "37ac68db-02ec-42d2-92bc-d7d2f4c33bf8" ; + crdch:id "100193fa-11a9-4abd-9bcb-b1688eefaf5e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008078-6166_diagnosis" ] ; + crdch:value "GENIE-DFCI-008981-6260_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f2c471a5-55a3-4180-be7d-c3560efade4b" ; + crdch:id "8fe03287-0b1e-4750-9006-58059562a243" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -1782,112 +1593,77 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "589f8f36-79a2-513f-a83e-cd707818b834" ; + crdch:id "740bf7b0-dfdd-4930-9cc7-3790cb8808c1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-HD-A634_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-MSK-P-0005212-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "34c0ddaa-1fcf-4e5c-b5bf-7cfae596c09d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "6e2561a0-676c-4f69-9059-d49696a56c64" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c25592d6-b3d3-47b6-a3c5-3cbc81803152" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "6176f8de-0835-4f23-9ce1-85511ac4e1f9" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD7774_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:50:23.633804-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1bae9a44-1ce3-45b1-9902-40faeba58120" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "bcecf093-e764-4c32-81e5-619d0e86216e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9b75ffac-0af8-40a0-9cc6-8472fbe942ef" ; + crdch:id "a00585d3-91dc-4976-87b6-d00c7caf5f5d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015763-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0008528-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d02e5c34-3c1e-4a7d-a67d-c2525ac3a734" ; + crdch:id "89fa0392-487d-4839-9c7e-cb82312941c7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -1901,104 +1677,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "80571628-74cc-4067-b16e-40cc5b040560" ; + crdch:id "73fd5157-4aa2-5b2e-852b-889d058a6f8f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0020147-T01-IM6_diagnosis" ] ; + crdch:value "TCGA-CN-5366_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-02T20:58:03.565619-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "10e9e747-568c-4276-9275-1f1d7cb30f81" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a6576ff2-b9cf-40dd-8da4-ca829d762cc0" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-001449-6594_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:id "f3e5a16f-7c16-425e-8321-b6b19fd469d3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4ec8fe70-22ad-4f62-893d-f95d77dd37f5" ; + crdch:id "62fdf8f3-a028-453f-b27c-c2506be68cbe" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1906d9ae-58dd-4b92-892f-6ff61788d171" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005398-2604_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "adbb22ae-5402-4918-a4d0-b54e2f114253" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "111ad944-f78e-4ec6-967b-f05c49b49b1c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5976f296-bcb7-49a6-8db6-8620875f12e3" ; + crdch:id "af2c06c6-b5cb-4369-906f-727e8e00e459" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008036-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-DFCI-005169-1136_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "257963cb-44bc-4946-ac72-7a1bb02f6af9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "104530ac-b606-41bc-93e4-5734f176d3bb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -2006,53 +1790,116 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] a crdch:dict . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0b151db5-f3df-4cc8-9bf3-049308634116" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "7c9e489a-67bb-5aef-92cb-b776ab07f413" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001794-T01-IM3_diagnosis" ] ; + crdch:value "TCGA-D6-A6EQ_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2da79fb4-bd1b-4518-a6a2-6159251d65fb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "041d7de0-fdee-4f6b-9945-058f8bab509c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "094085f3-01f3-4992-b559-832c897a704f" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003374-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:text "Not Reported" ] ; + crdch:id "43a91c60-f1f5-4b10-b0ee-c55afadac481" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e868826f-a629-4839-bc5f-5383b74aac12" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "37e8e5f5-0edb-420a-9f32-a2e167ef4cf4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "12d5265d-8eb5-4122-9e4d-976bdc0ded08" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0002469-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ed3acbbc-fb24-4be6-b09c-e0b6f4d9814f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; @@ -2065,9 +1912,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "18d9c548-2f10-5116-bf59-05cc53b3b5c6" ; + crdch:id "b23327de-182a-555c-9323-77d5bd3dd453" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7410_diagnosis" ] ; + crdch:value "TCGA-CV-7415_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -2077,7 +1924,7 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a24e0ad7-668e-4bc7-ae3a-94964278a407" ; + crdch:id "72f5520a-28f0-4be6-afe0-6bee4de5b69a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -2085,244 +1932,219 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "acd6cfc3-412b-4f61-a2c7-013c61fa2efe" ; + crdch:id "106c7016-9bf6-415a-a0fc-3722a1aaf2c6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "843ced6e-a9be-48ea-9313-13aa752dbbe1" ; + crdch:id "b7d03ca7-f518-4587-a54f-03896e53b167" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ] ] . + crdch:text "N2c" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d284c064-ed2c-5741-b1ad-2f9fd34b6636" ; + crdch:id "f7e49651-4dc5-50d9-af24-de743caf866b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-5153_diagnosis" ] ; + crdch:value "TCGA-CR-6482_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2f668e36-b359-488e-b0fc-fb7bb479f485" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3a24aaeb-37ce-4508-81d5-e531aac8a167" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2dc7070a-9c70-4bb1-9634-8c934bb9c8d1" ; + crdch:id "92173f97-b46a-4950-8cd8-6729ab9522c5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f079e825-160a-40d5-97cc-1931f11c4e2e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a8a92864-8cd0-5e1b-8451-ca6f3e84a857" ; + crdch:id "0b894a71-55ca-4246-bdf3-4d36622b203c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A6V9_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-MSK-P-0007622-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "30ad1a00-b48a-47bb-8cfa-d65e4c4ba125" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "8b9e009a-6ead-4105-a148-8c8a44be0658" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "9b60705b-95c4-4079-a907-e4a4b65a3cf4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "a4f6276a-b3cc-45f9-9fb8-30edd56ad4ea" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-011620-10763_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "462748e0-b611-44d3-b3fd-efb762ba317b" ; + crdch:id "d697e728-9813-4ff5-83eb-c7d814e07bcc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "efe7297e-9961-4ac3-b247-a9322e18240c" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD16071_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:38.104730-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "542b7dd6-20ad-4719-bece-768060ddab97" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "45ebf5cb-a072-582b-8ace-7cd198806bc2" ; + crdch:id "ac0363ed-feba-5584-802a-a8bd096fb07c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-F7-7848_diagnosis" ] ; + crdch:value "TCGA-CN-6022_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -2332,25 +2154,25 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f7831fa0-1f1d-4623-aba0-8117b925a1ee" ; + crdch:id "3b8fd8fb-429a-47ac-8b99-ae42a3fe968d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b99fa26a-da90-4b98-bea0-f0c71a1b6ea3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8aa78dee-bc22-4d4b-86d6-60fb80358da8" ; + crdch:id "952f71e6-b64c-456d-8d00-45e4118fef96" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d452d59e-92ff-46ee-840d-df8a161ca9c5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; @@ -2360,140 +2182,137 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cf36baf2-10e8-523f-9dd9-0f9c938be574" ; + crdch:id "4bcd5e25-adf6-5fe2-b07f-05d72b7b22a1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-4223_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-P3-A6T6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Gum" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "82db742d-885d-4788-b509-474715ae183b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "6f0b02c4-6efb-4104-89e1-2e76811b6afc" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3285f0ab-61e2-4235-b0ac-af1718ca1874" ; + crdch:id "3147ba3d-b1fd-4e40-82e1-56429f2389d6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "75430612-09bb-4d6f-9304-62a5b517d424" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "127b2222-93b1-4870-93f2-867d8e69d015" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -2504,23 +2323,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "982f892f-104c-4948-8788-6c77775e53a7" ; + crdch:id "ae2f70f2-dd19-493b-b6ea-bbe2cbe507cd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-013165-23146_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0014898-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:42:39.927651-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "27e33c39-2025-4573-9b0c-1bc774566bfa" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "d7332e8a-d17d-497f-9b44-cc7992f48739" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -2528,707 +2347,24 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f44a9ab8-f121-59c5-8087-567864266629" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "78608de5-dd5b-43da-8934-e0b6fa924ab4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A63Y_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-MDA-4493-11651_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "daaeaef7-3f0f-4155-908d-9aa6e536f94c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e0b45d74-3b6e-424f-86e7-2174d7c1245a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "50cca7c4-4586-43cd-a59e-3fdc646f5aba" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; - crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "b62e9fa2-da66-5eb2-b390-96985bc92b6b" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-H7-A6C5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; - crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "069b94fd-00fe-4073-bfca-3a3a8057d1f8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "875069b7-9411-4fb1-b8a2-992a052bee49" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "9b557922-d796-48bd-b194-1fba8622f254" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "578cf44a-2d2c-416d-a428-69547378bb9b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c061cf11-1e3a-5906-b58b-2b5530a456fd" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-6870_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5bf05a41-3a19-445b-96bd-439b9cac01eb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-23T13:20:20.149518-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "cc1be5d1-ea6a-4e7d-822b-51887dab88b6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e6af426a-d899-44ef-96a8-92bd76a0ea3a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; - crdch:system "GDC" ] ; - crdch:text "M1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVC" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1b2f7aa9-bc17-4cfa-8d93-b5a7bdd68bfe" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015451-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "8a18a085-a8a0-4fd0-9468-33e10fe1c55d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "748313dd-50be-45e2-9d94-75752dd6e783" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD10965_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:58:58.476597-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "97354824-7fe1-472e-ac48-74ad10e5da51" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "27fbdde4-c58a-46d7-a96f-918b64fe5b51" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037700-159036_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:26:11.717995-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "50b8e07c-b892-4fac-bf59-9e093e2d74d3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1e1fa97c-cb95-5810-9f22-9af6a0a42ce2" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6480_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0c6b4631-381e-4b73-ac9e-62bbc1849ff4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e49031dd-14f3-4f2c-8457-d0249c491ae9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; - crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "90bcf4eb-dd05-5d4d-b666-6947b36143d8" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-A6ES_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f99dc3bf-e91d-4011-b62a-2653b53417f0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "59ddae84-32f9-40c0-9d9f-e3b883ab5c47" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0ebb072d-0596-4deb-8607-2548b0396fb0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a84b9519-37b2-4311-ac32-8151ae7261e7" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-090167-282584_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:52:12.528526-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0f1ec484-9205-42f4-9696-815dae75b073" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "30984445-18bb-4b5a-be50-8bed548e6e00" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007662-3905_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "46f8b134-ad13-42d1-b3c7-6b2d8cf77f90" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f73d9c17-c497-5025-84d8-e9adaf48a245" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-MT-A67G_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "6b690841-3ad9-4919-8913-8f291ee95868" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7206e2ea-ad1d-45d4-ba3c-fc1f39fc52ea" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "25588932-d586-4a17-b18e-4ede4292ce9e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5ddc8873-1487-4787-8a1d-3b116a2db42a" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010816-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e179e193-0933-48cd-98fe-aa4e21c0ad44" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "d0d35a5e-572f-4cae-a0df-67ce30803048" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD14308_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:41:59.431029-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "32112d7c-2b29-485d-86c3-6b995450ec8c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "8955be34-dfc4-4a5e-9636-f27ccef4318a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; @@ -3241,47 +2377,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a0943f40-a682-4318-bc07-eea80150867b" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037288-116439_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:26:11.717995-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "8449ccd3-033e-4c9f-bec5-9f341264e12b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "be57683f-0245-4929-89d2-98740dc99b8c" ; + crdch:id "43212ae1-0d0a-411e-8ae0-61de91147afe" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-011271-11674_diagnosis" ] ; + crdch:value "GENIE-DFCI-006740-7890_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fe032782-a750-46b3-a282-26e110ed063a" ; + crdch:id "5f316e98-9980-4841-b297-f07b3e87004f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -3290,272 +2399,126 @@ crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "11688639-0783-576d-ac58-40e8e3a19be6" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A49C_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; - crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7758f04c-0e07-4e8a-882d-ece76469f433" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "34b36112-f260-4bf4-90b7-0cebc5988b59" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2b3b0e72-0926-5ed2-89c8-ffa1585d111f" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "748313dd-50be-45e2-9d94-75752dd6e783" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A6K1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD10965_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:58:58.476597-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "09b49e67-34d8-496e-b42a-5123fb516cc0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "97354824-7fe1-472e-ac48-74ad10e5da51" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; + crdch:system "GDC" ] ; + crdch:text "Malignant rhabdoid tumor" ] ; + crdch:id "33c5c040-da3f-5e5f-8d13-ab9eff88f833" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TARGET-52-PASCDH_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:system "GDC" ] ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:system "GDC" ] ; + crdch:text "8963/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "43115789-cca5-4dc0-8377-e47b90c3f16f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "1d3eef26-a725-51f7-95fa-139d1a7da76e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Blood Derived Normal" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8ae503f5-a283-4bdf-8c82-de63f534bc85" ; + crdch:id "da724216-c1fe-5420-9e73-3a9d4b52bf1c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Primary Tumor" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "unknown" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5a687c66-0c8c-5e23-bd7c-6988abb14d66" ; + crdch:id "972c3046-1f6c-40fc-a83a-3b200148a683" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6021_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD5830_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f1cbf326-7657-4c9b-9c8d-e2036e89fd07" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:05.012118-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "edcbcb1d-23bb-4177-8f77-71071822cd89" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "ed2a5846-de67-40c3-9074-3adc9edfb0b0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "619a1a7c-f360-4e07-aa85-812e2b1bd92f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d68e9ec8-d562-49e0-abf1-ebc41a0f439a" ; + crdch:id "f87fc232-ea15-4a26-a863-8604cdb8bb06" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006509-3496_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-037287-88492_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3e441a98-f869-414d-9732-4b4037711d5e" ; + crdch:id "421f819b-c4ac-445f-882d-c36766f7002a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -3569,9 +2532,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2457e378-c4bb-516f-8966-82e1453eafd7" ; + crdch:id "5d8267c6-4156-5145-b6e3-49c68f8cabfb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A460_diagnosis" ] ; + crdch:value "TCGA-CN-5361_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -3581,34 +2544,34 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "904d5793-ae7f-492b-aaed-ea6cca865d63" ; + crdch:id "c807171a-4433-4246-a454-c5cf768da8aa" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b1c47b2e-ba48-4f1f-b07e-f930b1135201" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9e397756-8535-40f2-9fc8-d0f1392a5e6d" ; + crdch:id "2877214f-4aab-46cf-b052-b6e7d2662ff5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5b2581d8-c087-4caa-b9ce-bc0168fbfefa" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], @@ -3618,86 +2581,50 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N2" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "81f6058e-7aef-4ed0-b7c4-a0f1ff8a52b6" ; + crdch:id "f543ba05-0134-4222-bc49-da336358e2e0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-036373-130403_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0005862-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "3b018cb9-12c9-4445-b021-1fc93e0f74c2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "c975f49b-ba03-4e22-bcf1-7aef636601ef" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD3546_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:01:38.093247-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "42ef0174-6a5e-4804-ae6e-5d0122cb51c5" ; + crdch:id "fbb548d6-a035-43c3-99a4-7fb2892ade49" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -3709,74 +2636,113 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2fcaff59-bc46-4971-9a75-dcbf2c85a5ca" ; + crdch:id "3f9675d2-ad2f-5a88-af81-e7e9b5744c1a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0013498-T01-IM5_diagnosis" ] ; + crdch:value "TCGA-CV-7437_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1c156e43-c8c3-4ecb-83ff-2075ebd89cd7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "46be59da-3e8e-43cb-a4f4-6658b12f1fe9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c96ca96a-8046-4381-a767-1119705c5500" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008037-6376_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:11:14.458475-05:00"^^ ] ] ; + crdch:text "Not Reported" ] ; + crdch:id "215c17d6-2035-48da-9d06-c54734042898" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d7340d97-4ebd-4125-961a-9a5abe2f0ebb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f5e6b025-48ca-4fd5-b657-ae622bc9de02" ; + crdch:id "58c15c00-ddad-4f65-9f03-1882b7f9a09b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a00585d3-91dc-4976-87b6-d00c7caf5f5d" ; + crdch:id "de3c2719-988d-4266-98cd-c1139a2cc412" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008528-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0006641-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:02:01.981535-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "89fa0392-487d-4839-9c7e-cb82312941c7" ; + crdch:id "4e6ffe6c-feee-4dca-b56d-0f2c8b498ae6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -3787,29 +2753,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "b0179bcd-bda0-42ff-8654-61f3fe576e73" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "04081703-b701-4765-8309-0a204a48c183" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD12050_diagnosis" ] ; + crdch:value "GENIE-VICC-201710-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:03:00.815411-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0a8dd963-c724-4a77-b662-5f711ac88607" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "cc51bca3-858a-4ac3-b48a-c4d273b2329c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -3820,20 +2783,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ae2f70f2-dd19-493b-b6ea-bbe2cbe507cd" ; + crdch:id "26bc85c7-5376-467d-a880-4c415ba3b3a5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0014898-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-MSK-P-0014015-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:42:39.927651-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d7332e8a-d17d-497f-9b44-cc7992f48739" ; + crdch:id "968b2133-a7b0-4d2f-8949-f6ff299f1219" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -3844,29 +2807,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "583cb32e-5e1c-4f3a-bdef-035629e3eb57" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "576b4319-20fe-4dd8-82b1-c34a70bd2182" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5451_diagnosis" ] ; + crdch:value "GENIE-GRCC-596e5ce8-metastasis-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:40:28.865821-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a8ae1d5d-04b7-4012-9bf5-70a664f325ee" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "7889cf51-be9b-4193-b057-5f348fca10db" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Not Reported" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -3874,199 +2834,122 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "47de90b5-a5ed-5ce0-ada8-7f2c8e621913" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "b0113a66-8202-482a-ad65-dc55cdca3c27" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A641_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD8711_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0c14d932-3b44-48fa-8974-db6e01464851" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "cc3866fe-2690-4354-a548-10189054b85d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:47.854910-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "744cbf84-554d-4cba-aa4f-4c1e5e28a1ee" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3ece7ea7-cad2-4e6d-811f-c91f63a4fca9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "72d80059-302c-57fe-89fa-10045543f0ad" ; + crdch:id "7c7482aa-6349-58c9-ab17-6c69acbd579e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A6V1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CR-7388_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b2ad9679-048c-43c4-9d78-45638ad5a493" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "c6aafc51-6295-494f-9bf2-1e4f43a72ae0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8f952c62-2404-484c-b8af-33ce60f4e024" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "f27e3255-bc73-4943-8201-5245b85c4ee5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "N2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; - crdch:system "GDC" ] ; - crdch:text "N2a" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1dc5e826-3f32-4d4d-8e2c-00fdbd76b393" ; + crdch:id "0e732992-a174-4861-8e05-a6c3e21107b3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010503-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0001903-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "78c3f61a-5719-4604-8ebe-c21057d3e416" ; + crdch:id "ea373411-6d3c-4ee3-b8c1-d79131847aa1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -4077,26 +2960,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "6252ba82-08cf-4a88-892e-bd2847842225" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "40d016b6-27a3-4e33-ad6b-f50eaa54e2fa" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0009588-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0008097-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0fd4a1fd-2313-475e-ae01-d424516e42c9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "f71f4733-17f4-436f-b12d-bad5b99ceba3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -4107,97 +2990,47 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f0a3480b-d52a-5db1-b03f-693a9bad5cfc" ; + crdch:id "e4e39ca9-5e45-497f-b616-8e4d9edf9431" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-5559_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-GRCC-3876b32c-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "fbea64f9-b46b-4af1-bfb2-1791d93977b6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "43fbb037-8ba4-4ba3-8458-71a027eda822" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8c925c97-a7e0-44b3-ac62-b365e89975f0" ; + crdch:id "59d867e0-1111-4114-b47d-39b108eecf06" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "192c4be7-66ba-416a-abfb-1a88e63e7be4" ; + crdch:id "5ba2b63c-b0c8-4304-820c-9b04ebb5a7fc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-534918-unk-1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-DFCI-002837-2078_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:05:42.341898-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e15f8344-5f7f-4602-b2e3-8fcb0418cb8b" ; + crdch:id "fb20acec-aeb5-4591-b114-0834c6629db7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -4211,19 +3044,19 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b23327de-182a-555c-9323-77d5bd3dd453" ; + crdch:id "95d85e5a-b82c-59f8-b7ad-710e019cdebc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7415_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-TN-A7HL_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b7d03ca7-f518-4587-a54f-03896e53b167" ; + crdch:id "1077bf93-cf23-41db-925c-c633921894cc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -4231,14 +3064,14 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "106c7016-9bf6-415a-a0fc-3722a1aaf2c6" ; + crdch:id "4a0d79fe-9eb9-456c-b483-ccf956597a3d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "72f5520a-28f0-4be6-afe0-6bee4de5b69a" ; + crdch:id "9c02fd4a-a29a-4a44-ba96-5acb6ff11f7f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -4248,433 +3081,336 @@ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b8812861-0e19-58f0-bccf-667970cdb04c" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7399_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "05c3d8a0-47a2-44b2-b0c3-144ec0cb2673" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "3dd4255a-7359-4b51-8a0b-44d9e249956b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "80c00d5c-1297-43e4-bbcc-cc895915ec2a" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-51823bc5-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "8d24d0d3-ec37-4b8e-9c31-e23965637da9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b7c4b294-1897-5001-8494-cedac0a7f991" ; + crdch:id "3896106f-2770-565a-b872-0d61198bb107" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5440_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CV-5442_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Palate" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "28780b51-0b53-4d73-b399-ec90b45de0d3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "ec885af4-3513-4790-ab1f-6ecc94b6115d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3f9a9578-e8e6-47b7-af7b-31d9cffbfd3a" ; + crdch:id "26243d14-e401-4ca4-92e7-aee13c9e6e47" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d773747d-fd09-4890-a436-9b212e19063b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "698208bb-7272-4ad5-9cc0-909cb669bdaf" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e68bc170-6152-4c90-9b9b-e31856495716" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0005506-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b5f4b393-678a-4964-b625-19c8099cde13" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c652d5fb-652f-485c-99cd-4e3e00af1126" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000396-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2bde1811-da29-46e9-973a-45ea43387818" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "af8fdb73-f4a3-5b32-b9d5-6f9d39a97856" ; + crdch:id "0501e7a7-232b-58be-9425-92f1ccd697a4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-6824_diagnosis" ] ; + crdch:value "TCGA-CN-4727_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "10c45c93-36f6-4085-8bc8-f46dfdedca1f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "cc2d6cfa-7640-44dd-a200-68fd9f9ee69c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4d8bbfbd-1a39-4630-a1e5-3bc6abb01949" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "a7257360-c4dd-4f59-bfb9-c8d593050146" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2e1366b9-95b7-4a0d-81f0-7ec14e4f4592" ; + crdch:id "f102aef0-94b8-4d26-8055-35b76da9dd5f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c1887ffe-1e7a-4584-a9cb-897604949138" ; + crdch:id "c239680c-7353-50f5-a155-33973562e904" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD7475_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-CV-A45W_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:48:10.807261-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b82784b8-217d-487f-b2f6-4435ebc09885" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "fe66156a-b3ea-4ed1-a5ca-68a3664c3505" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Not Reported" ] ; + crdch:id "7202ca4b-6caf-4f4d-adc9-4c59b00cbdc3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f9ae08e7-9166-4699-801a-4bed11f72dc2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d2a0bb97-195f-422a-969f-0342485cf8c6" ; + crdch:id "d0678ad6-4a4a-4ec8-9e5f-352c1347efc2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010743-8938_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-a8pxs0u6-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T18:19:50.810302-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1f6b16e8-e1f4-462a-ac25-700c915f464f" ; + crdch:id "ab9d819a-6445-4bad-a520-3d1edf413508" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -4688,9 +3424,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a47bda97-0952-47fa-9a6e-277baa8762a9" ; + crdch:id "85d63c6e-a6c1-47a5-92a9-216719073a4a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004713-938_diagnosis" ] ; + crdch:value "GENIE-DFCI-004072-413_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; @@ -4701,7 +3437,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cc589138-6e86-49ad-8d76-857543c02842" ; + crdch:id "9a26d9df-9ab2-48df-ada8-8bd8455cccd6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -4715,50 +3451,109 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ea4330da-9d29-4e64-8197-55a50ee283dd" ; + crdch:id "066a4a47-3b4a-582d-984d-476fa8a4fc57" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001557-T01-IM3_diagnosis" ] ; + crdch:value "TCGA-CV-7422_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "90c9d5f2-ca54-4084-99e7-e9407e364b12" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "2c2db97c-8c8d-4f1e-ab73-469238609d61" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "63bdeeca-a7b1-47fb-9945-c24f7513c56c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "9e25f49c-cd83-4171-9e07-51aca3fb1019" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "35adcfa2-f4ae-4aec-8362-097fab231545" ; + crdch:id "f9a0b1dd-a13b-4a14-ac22-c9570e02ca60" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-000205-461_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0008792-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ab00664b-8f6a-493d-b000-89f1341dc713" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b882dbe8-5494-4092-8bad-ccca6b119775" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -4769,189 +3564,191 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f351c260-09d7-594c-8347-292ae6f65f1f" ; + crdch:id "2602d676-8c2e-5bdd-9790-a0a072d3f670" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A49B_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-DQ-7596_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "16b91d52-3168-44d9-bbbd-9f6e8b2582b6" ; + crdch:id "61c82e56-e64e-4fcb-bc5f-dc4fe34b6c58" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a49128ea-01e4-4587-845b-6b26bafa1c29" ; + crdch:id "7a94106d-5604-4b73-9c54-54a72b12f52d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f662e970-6a51-4164-8458-61e7ff054806" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], + crdch:text "N2a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "c975f49b-ba03-4e22-bcf1-7aef636601ef" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD3546_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:01:38.093247-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "42ef0174-6a5e-4804-ae6e-5d0122cb51c5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "fcd7326c-3bf2-425a-b117-f1e5f6910db9" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-c9c06784-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "43bdb66c-6b5a-4a1c-9d44-2717ecc981ed" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0b9b2b22-2fe6-5569-99ea-4647a15e68a0" ; + crdch:id "0cf011bf-054a-4eea-aacc-b963ff83734a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7177_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-007960-5976_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e850a80d-1b50-4ab6-ab36-1d1a5e697d7e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "768e2bab-347b-4d90-887f-bf5692a91eb0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "c353a3fb-dad8-4a6c-acd3-4121eb21b98e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "ddb758e6-20a8-4a28-ba98-798de978154f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "4dbbefaa-8e8e-4a44-943b-48687f123673" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0010088-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "21152590-1224-410e-aaf7-4088302c809f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "b5da1115-1fe3-49a4-892b-ef43e64dbee4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; - crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "232f3bad-3cb2-5b4a-91e2-71f37a7eff72" ; + crdch:id "843f33f9-e390-52bc-90c8-fba0a4557916" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A71B_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "TCGA-UF-A7JV_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; @@ -4959,51 +3756,51 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5c464f43-4aa0-4203-8828-5fc4cb13cf42" ; + crdch:id "c312a7a4-ba29-49a9-b4dc-876505a6a6c4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "df66e44f-3130-4d7b-a1d9-2d90f96b4c7e" ; + crdch:id "eed0dcf3-36a2-4890-bb02-e8b56ba4d8d8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3a4af2fc-6443-4644-9da0-fee722e6d5c6" ; + crdch:id "a1d62ba6-696c-4693-9067-d4226a4e6316" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; @@ -5013,230 +3810,299 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage IVA" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "cf507905-7cf2-408b-a08e-b703df54147f" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-NKI-DYRQ-CX3U_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "36b762ea-ade4-4e7a-b824-0fdadd0e33ef" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "9b998038-9a23-4348-a5f7-e2d3126e118c" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD14936_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:46:29.991257-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "fc50dce3-ca12-4a52-a8fd-27dcd3887746" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1ddea2fe-7874-5d31-b1fe-2cb2b0de542f" ; + crdch:id "bfc1721c-c0de-54b3-9170-781b78cafd44" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-KU-A6H7_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-BA-6868_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b4074f91-5478-4117-bee5-ed164e4d38c2" ; + crdch:id "d660bc61-4016-4f52-98c3-72de5459946a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e4439379-d930-4b9a-b498-3b75e569f8ad" ; + crdch:id "ad04d034-7fff-4073-8c1f-97fac3d0bbdb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "840d3da5-0493-460a-b5a9-4285e1a2ad37" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "61eec5b6-925d-434b-a318-b22fc21c9ffe" ; + crdch:id "0469c4d4-58ff-411d-9bf4-8d8bbe31d7c5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; - crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; - crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "N3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "18d11972-ed5f-4c5b-9511-18b00bca7f7d" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MDA-8036-18260_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "475098e0-9927-42fc-adf2-e280d8aec3bb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "8932404c-6adc-4b1d-81fb-fdb4dbb32ddd" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0008185-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3a9e0ea1-fb4f-47bd-bf6c-831f7101b005" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "491f9f68-fb39-4d17-a75d-90d14e801df2" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD15095_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:44:57.662014-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ae6cd26b-98b2-46a9-917b-cecd94358907" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1da5c51a-ee25-51a6-a4c2-27d8fdcbe24e" ; + crdch:id "2b051980-b5b7-4b1d-900c-9705c24b2a78" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5365_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-009287-6605_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "665d66ad-54ee-478e-bdd0-85d77980fb3e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "665d4bff-603c-497b-816f-c98784665d0f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1ed245de-fea4-42c9-9197-773bcd12d2a8" ; + crdch:id "781e0bea-f234-496c-915c-c163fc8de24b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVC" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; - crdch:system "GDC" ] ; - crdch:text "N3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; - crdch:system "GDC" ] ; - crdch:text "M1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N2" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e4e39ca9-5e45-497f-b616-8e4d9edf9431" ; + crdch:id "e7406302-5dd6-45b1-ae98-a8094c495943" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-3876b32c-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD13780_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:40:26.338588-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "59d867e0-1111-4114-b47d-39b108eecf06" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "c9bccdb4-1bd0-44e0-bfb0-7588611ab01b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -5247,67 +4113,62 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "37b4b703-52d6-51dd-9cd7-3f759862a78c" ; + crdch:id "92f6368e-51fb-56bf-a72d-7ccc16eafb44" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A63W_diagnosis" ] ; + crdch:value "TCGA-CV-5434_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9b9dbf11-d017-4723-a76f-c25ce4a01f09" ; + crdch:id "dc649d39-482d-4855-b9e3-129552e5e421" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8da610b4-0a32-4ef8-9f55-1c969addd79f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3f70e2db-b313-4f3f-89e7-cd1c0acecf9b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e6cd0e23-4423-4ebb-b314-913419340811" ; + crdch:id "657cf588-cca0-44c2-83b3-0e87f7a81f29" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f6130e55-1627-4d2f-bd8f-c0e778a1aa45" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], @@ -5323,36 +4184,42 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fa79bd3b-f6c7-48c1-93af-5b6fb08de876" ; + crdch:id "396ba806-81a2-43e2-be95-276cdeee09e3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003292-1283_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0003049-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a3eaae17-ef1a-442c-93cc-0fd82a8887bf" ; + crdch:id "162d69ba-adac-4884-9d98-3bc70cdb72a7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -5366,77 +4233,107 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c1551a30-c8b7-4ba5-b5ed-044b55587a38" ; + crdch:id "bd3c4df6-90f0-58df-8713-51ca36d74124" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003078-318_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-A6V3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1647be39-e387-4457-a1c0-83483d25ea5e" ; + crdch:id "285e2354-8efd-4951-87cf-0e188d11423e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "97657453-6a97-4879-9440-fd0eea9d5f33" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e978fb2f-2b7c-4ac7-b4c0-fa527f8c4ffb" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-090186-282458_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:52:12.528526-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "1bee9751-cbcd-46d2-97ac-bbe9f4495f2c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "09912a9d-8fe7-4170-89cb-f0881ba681bb" ; + crdch:id "cf973339-e31d-4fb3-833e-f954634d95ee" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037012-88553_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0014965-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:42:39.927651-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "89c7b64b-262a-440c-b2b0-b45a94097d6b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "1bd46cb2-e563-4a48-a36e-ea4f7a15173f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -5447,23 +4344,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "de59133c-2442-490c-9f22-057c8a47ff70" ; + crdch:id "30984445-18bb-4b5a-be50-8bed548e6e00" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008518-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-007662-3905_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f4e28471-79a4-456e-bba8-db331560bdb0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "46f8b134-ad13-42d1-b3c7-6b2d8cf77f90" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -5474,9 +4371,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bfc1721c-c0de-54b3-9170-781b78cafd44" ; + crdch:id "2c09a792-df0e-513e-a9a2-7e363de6435e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-6868_diagnosis" ] ; + crdch:value "TCGA-F7-A623_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -5486,88 +4383,121 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d660bc61-4016-4f52-98c3-72de5459946a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "5f14a8c0-f19e-4a67-b6dc-907196ab34f6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ad04d034-7fff-4073-8c1f-97fac3d0bbdb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "33c19ae3-107a-4b64-9906-5b775025cd8f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0469c4d4-58ff-411d-9bf4-8d8bbe31d7c5" ; + crdch:id "bb90f8e2-c872-4ded-9d10-5110f023762f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "696fd614-355c-42d4-b318-9d4a0d23ee17" ; + crdch:id "d113feec-68eb-4294-b6b4-6b8e22ce56bb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-001641-3996_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0016562-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:49:52.836213-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "14dd72d1-596c-42c6-a5aa-c3220dc6fc21" ; + crdch:id "99c1a34d-ba04-462f-be28-bb5eac77b316" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "826319f7-67b5-481a-998b-781e3ded01c1" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-22f8acca-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7aa50a3f-dd6c-496c-89e2-2d8d6d136acf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -5581,161 +4511,184 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cbfef8ff-181a-4048-a571-f78fd34799ef" ; + crdch:id "eac797ee-ffad-5c80-8f0a-7e95590e118d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037220-88689_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-7389_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9f95c03c-4c29-47c7-8bff-47c3014a61b5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "9c35c1ec-5ca6-4900-aa39-ab1c962b9c4d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "6e926ab9-e086-48cb-876d-d490c46cb7f0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d852d062-d7e0-559b-8492-da2b0abe8415" ; + crdch:id "3f0b65d8-182e-57af-87b9-29e59fcdaab4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6470_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-F7-8298_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "aa121605-a2c9-43fc-a836-8ec6c42b99de" ; + crdch:id "94c71079-a453-4a4c-b52a-ab686bc83b65" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3f2ed4ae-5b71-48d9-b120-4f7bfd4b34c4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "afb7ea63-2959-4e53-95ea-7a032dcb5a8b" ; + crdch:id "8f5a4b47-4c69-4295-a576-fd3e558754a5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; + crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "stage i" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; - crdch:system "GDC" ] ; - crdch:text "Malignant rhabdoid tumor" ] ; - crdch:id "9a11a042-337d-5a91-b483-093f98b0b72f" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TARGET-52-PARKKN_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; - crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; - crdch:system "GDC" ] ; - crdch:text "8963/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "ced7edc7-a9ff-5d30-a63d-dbed4edfe497" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; - crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "unknown" ] ] ] . + crdch:text "T1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5c70e571-fbe5-407f-aea2-9f740e6f5d2a" ; + crdch:id "cde79cd2-3aab-48ed-81a1-259a3cd21002" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-002399-7809_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-VICC-122614-unk-1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d57d8dd7-f0d5-4c3e-9ac7-cc23e2aa77d7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "71ba3119-c343-43f0-84db-4ba8787d316b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -5743,199 +4696,198 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "e89ecbde-44e3-5db5-be20-af6cddaa4e92" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "1da5c51a-ee25-51a6-a4c2-27d8fdcbe24e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-T2-A6X2_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "TCGA-CN-5365_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fe1541c0-a239-428f-bf43-8b8b999d362e" ; + crdch:id "665d4bff-603c-497b-816f-c98784665d0f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "161b6a0e-0b50-41a1-bdf3-bd7666067454" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "665d66ad-54ee-478e-bdd0-85d77980fb3e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0080b5ac-b9b2-4fef-ae51-6a6178325364" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "1ed245de-fea4-42c9-9197-773bcd12d2a8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Stage IVC" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage IVB" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "N3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ad265c45-3ba4-4f8a-afcd-70d7f2e79751" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009344-6546_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b993e287-e823-4843-b182-3bf775dfb489" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "stage ivb" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "8a0ce16a-46ec-433a-9679-e76ca74240fc" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5506_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:41:09.015209-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "14f00898-8aaa-4008-9eac-0959333c3525" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "M1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0ab5d8a1-108f-450c-89bd-efd0c4d285ea" ; + crdch:id "4d192f26-a2c4-537b-b8b5-1473a759882c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003059-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-UF-A7J9_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5df6c457-baef-451d-b1cf-eb7fa6adc602" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1303ddf5-cd55-47c9-9f93-c09d7bbf2f80" ; + crdch:id "5be42d60-80c3-486f-8717-801fec0c89d3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "fbceb407-e7f8-4942-8689-854f8999672c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5db2900f-3088-48fa-ad1c-8dbba6bedbef" ; + crdch:id "696fd614-355c-42d4-b318-9d4a0d23ee17" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0017777-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-001641-3996_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:37:32.909734-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "dc326cf0-cb20-4f0a-968a-28c6923319dd" ; + crdch:id "14dd72d1-596c-42c6-a5aa-c3220dc6fc21" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -5946,68 +4898,49 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7c0c3290-5b41-50b4-b37d-536ebbac2af8" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "b07c0682-d50b-5680-97fc-8e709e21c064" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7101_diagnosis" ] ; + crdch:value "TCGA-D6-8568_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8071/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f040a5a4-e955-4e69-9f2e-ae9a4c78780a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "79ec5357-3a44-40db-a1ba-ee282b484526" ; + crdch:id "eac181d7-f8b8-4350-92aa-62d3fd1bd86b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "397b08f6-f560-418b-a6e6-2d953187bd5d" ; + crdch:id "6f150e98-8b4e-44ee-953b-1692d76c8868" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8e461b7f-1bfd-476d-a948-7aadb89a41e5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "c812093b-04ce-4d3f-841d-9b81de63fc38" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; @@ -6020,12 +4953,18 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -6037,250 +4976,331 @@ crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ] ] . + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "640dafcd-ca8f-4305-bd40-240ff476b75e" ; + crdch:id "24058118-f7b3-53d4-b24b-07a2ac2e66b1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006707-2784_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-5369_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Palate" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "53e7103c-42c4-41cc-948c-b8e23271bee9" ; + crdch:id "11d697ec-f451-4102-a908-e44f48ab0800" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1ebf1ce6-31bd-4c8e-b3e0-f70d47cdc527" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0016351-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Not Reported" ] ; + crdch:id "8d31f35c-9178-447d-9a2b-acc305fab407" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "90f2519b-17ba-40ad-baee-cb711b306a91" ; + crdch:id "b4c02606-0f86-46e4-9daf-dc7dbcd60d78" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a69046f9-49c2-4846-a394-ffebf61b0340" ; + crdch:id "e792cf88-dfe7-5130-ab9d-df59b3ed1b3b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-001847-1155_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-7421_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ae00c91b-f03b-41fa-bd2f-d6fde4338cf1" ; + crdch:id "6766e43d-12fd-49ba-bdde-c19bb71d329d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "59ca6acf-5527-4fa2-8bb2-658029b9c67f" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009312-6572_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "667948dc-d9bd-4813-922b-69468835c551" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "20b2ca7d-bce3-44c1-a0db-ef271aca97bc" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD2717_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:id "40583cb5-46f0-4966-82c7-4149f14581d4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:58:58.753780-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "69907c44-c952-482a-a307-44efd82a16dd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "ef81caac-1fdd-43dd-80a3-4e18eb35271e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b9143400-abdf-5f03-9771-ebafe5bb5d43" ; + crdch:id "a3c1a290-626e-5e1a-b120-0153a79fadd1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7371_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CN-4741_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Gum" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5a5005d4-6cd9-431a-89ec-ce6d34b0fc7d" ; + crdch:id "a47974a3-b37e-4041-8953-5f50f8745681" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "8d8ddca2-6461-4a8b-a696-da0906661b9e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ac9f5493-c06b-40dd-b80d-7be718d27289" ; + crdch:id "03c9108a-5139-4bac-9641-c7dbbedef420" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "75ebf700-6ff1-4980-a420-41df37dd2c42" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0018608-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:39:49.045696-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e4d9ec72-9281-4b2e-841d-06d84634968d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "9b998038-9a23-4348-a5f7-e2d3126e118c" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "64017f79-8293-4fd3-8af0-bf01eb6cf49c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD14936_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-UHN-653571-ARC1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:46:29.991257-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:21:56.842750-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fc50dce3-ca12-4a52-a8fd-27dcd3887746" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "5349f1ac-ad8d-437f-a9e7-30b2323bd11f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -6288,26 +5308,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "00fbc722-7387-437d-b859-3d35c86e02fc" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "c1dc41f5-0fea-42e8-afdb-fabc542d0548" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-040b2fef-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0005869-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "25007740-c3ea-41f0-a9dc-52de44cb9faa" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "bb6ae997-ee6b-42e0-ab0c-c9fbc64f8d9b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -6318,118 +5338,116 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "24e37f06-2587-52ee-bcb3-40688978538e" ; + crdch:id "cceca036-354c-59e4-ad7a-886865aada46" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-A6UM_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CV-7245_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ccc0e6ba-cf8b-45e4-9f0b-dd2422b3e470" ; + crdch:id "f0684e03-2d91-4e9b-9d11-a3063ccc2f34" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d455327a-a947-4a67-8fb5-44438abe5976" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "99404948-9837-40eb-bf38-c1cfe1b9a88c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "aaa6607c-e333-4f99-b1dc-390c3cad4f1b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c4aabbde-a46a-403e-b974-7b61b964a1b8" ; + crdch:id "c8ac9749-82ff-4348-8d91-5ce677697a15" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c70dbc51-07bb-49a1-bffc-ea639cf09e66" ; + crdch:id "a6576ff2-b9cf-40dd-8da4-ca829d762cc0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5893_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-001449-6594_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:40:08.863452-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3c1903f3-2a52-46cf-872e-060ba3a092e3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "4ec8fe70-22ad-4f62-893d-f95d77dd37f5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -6440,57 +5458,105 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f7e49651-4dc5-50d9-af24-de743caf866b" ; + crdch:id "be59114f-e2eb-4d06-824e-7aa867673eda" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6482_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-004755-1862_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "92173f97-b46a-4950-8cd8-6729ab9522c5" ; + crdch:id "255bbe44-dce0-4905-86bb-317144348172" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "e2403080-b7b5-4d13-b62e-9b7293a45058" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0002484-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "3a24aaeb-37ce-4508-81d5-e531aac8a167" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Not Reported" ] ; + crdch:id "89363cf2-b8d0-48cd-97e5-4cd68ed372d3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f50b7ab8-f114-470f-81b0-35ddd9246c46" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-034356-130499_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "21a0707d-357c-4ea4-aec8-1227b8997cbb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "9076e2ad-9cef-4efc-99d7-387d250445ee" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-025889-116451_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "678dfc0e-f085-4c85-b444-8fc1604bdcfe" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; @@ -6500,20 +5566,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9e0b865b-296f-481f-8bc2-7bfe4642d805" ; + crdch:id "83347eee-7d6a-4848-a139-a71f053e92c9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001912-T01-IM3_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0000768-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "271c4064-6b2e-4971-853f-e3f2a1cdd74a" ; + crdch:id "fd2acd96-a021-4fd4-b0f5-1d9f6e4448bb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -6527,20 +5593,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ed6cd70d-8278-4da3-9067-ab74bc051381" ; + crdch:id "d1841d22-3350-4037-918a-bb399ed85963" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007474-4132_diagnosis" ] ; + crdch:value "GENIE-DFCI-005202-1165_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7946822e-6d72-4013-8be2-f3ffb0487d65" ; + crdch:id "97064320-d382-4d87-a302-72490d7577d6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -6554,263 +5620,507 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a4f6276a-b3cc-45f9-9fb8-30edd56ad4ea" ; + crdch:id "52d5ae11-4bb0-53aa-bff7-31190888f8ff" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-011620-10763_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-5247_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d697e728-9813-4ff5-83eb-c7d814e07bcc" ; + crdch:id "950233c0-c1ca-4b69-8e3f-a6072dbc7e6a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "43739161-8083-4740-a670-1a334a87ca7e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "96e73819-3b05-4a68-90bb-ceb60d419d50" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "9d69f6a3-4edb-54e3-a840-ff1ff0aefb30" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006296-6704_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-UF-A7JK_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "51ca54fe-f436-4a88-a11d-ab0781666edf" ; + crdch:id "56c76698-7155-4f7a-9f9e-4fb62c673599" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "90e4a976-0d97-47ef-aa29-295c2afeb31b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "15776f80-0722-45a8-bc97-cc209cef631b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0c55f80d-c82c-4554-916f-6b117978b3fc" ; + crdch:id "9e74f3f5-ab22-55d9-a79e-9884f3b0f109" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000454-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-5374_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "27fb0ae5-d8a1-46ac-ad3e-2464c52d9cfd" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5c3a5e81-481c-430b-9c70-f2d61a77568d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "88000b86-9334-41ef-847d-6668d17ec62b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "617df1e0-b075-4610-b6d5-8850786fea70" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "07feaa02-95ec-48b9-83ff-ddd765c8ca9d" ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "00ed54be-bd0c-5950-9165-b08535ef9f18" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0006098-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-TN-A7HI_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:02:01.981535-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "eca4b442-f9d1-4018-94cb-158757bd3bea" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "9808b586-4541-42a8-a72c-0c043ff568b3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "10fdde54-4aab-4498-925c-38ccd8df431d" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015591-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:text "Not Reported" ] ; + crdch:id "2a081426-e4fe-4868-adc9-c14142490b81" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d2928928-ad9f-46d3-89a5-a00131eaec79" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "3ad15aca-9197-4512-8bb9-77099ae8f049" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3cb5d51d-2566-4b1f-ad4f-57520007e73d" ; + crdch:id "1fdbf271-8b0c-5d7b-bacf-d883e0d0d054" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-050743-203353_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-5360_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:18:25.269226-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c862481b-aaaf-41d4-9c29-188760a43dd8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "0c00768e-8b13-4b8e-80fc-b344740845f1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "0f72e73b-f462-4eef-9d1e-95e83c1f2aaf" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5362_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:05.012118-05:00"^^ ] ] ; + crdch:text "Not Reported" ] ; + crdch:id "9439bc03-9d26-454a-ba80-a0f5a4585656" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9f4929bc-09a7-47b8-9720-d6f829b51a13" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "740cef36-1319-4096-8ba3-8e6fce6282da" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "18a6869d-fcbd-526c-a71f-7f5145b12278" ; + crdch:id "b27a395e-c9b4-5903-afcf-90ba31fcdeb2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7440_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-HD-7753_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bb0c2fd4-8ffd-4825-aaf2-e865090940c8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "86b81c8d-ae15-477a-86fa-6e10f1263f87" ; + crdch:id "e723f1bb-73a3-4d65-bd25-de76138515e9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "80eca6e9-b390-4878-a070-e40c1c19b1f4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "7fb56f25-873d-475c-9db6-f0be3945d926" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-25T15:20:17.640379-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1d594963-b5c3-496e-af52-5f6dbcd6910f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "698f639f-c34a-4f21-8306-26002008804f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "Stage I" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "stage i" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; @@ -6820,42 +6130,60 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ] ] . + crdch:text "T1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9223ac2b-219b-423b-bd4f-5d28e84c8d89" ; + crdch:id "b5b027c4-6ae8-4c42-9ffc-46738ec336b9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-001409-5066_diagnosis" ] ; + crdch:value "GENIE-VICC-671452-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:05:42.341898-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fc3b12ce-4c74-4faa-ad8b-60ddde831901" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "eddc8197-6d13-4eef-bb1d-06d1b8df5395" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "e71fe2d8-2dc3-45b4-bc48-25b118a6f909" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD2206_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:54:31.122378-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "68742842-28e9-49db-b49d-79c73ad4ef0c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -6866,211 +6194,190 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7747a88f-1a9b-5833-9442-af0b1350bb4f" ; + crdch:id "8b48f2a0-f69b-547c-a9df-35b18ec7bb5a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6013_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "TCGA-CN-A63U_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d018cd44-6b01-44f2-9181-81153225aab8" ; + crdch:id "b4430e0f-983c-454d-926e-a33fcb4cd02c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c0c84016-117e-498c-9ed9-52e279e89e33" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "a6af965f-ae37-421d-98d6-a69ce62213ac" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8b510bc8-7b3c-4861-9a40-c2c30b7099e0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "812b8ee1-096a-40ff-914d-9957644b7d11" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "dc412cff-36a3-4721-b1f3-8e16ed74489d" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001186-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "1853a05a-8846-4da3-9509-bff587eb6e8d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "dac87ff6-12f3-553f-a6cb-fae679002ff0" ; + crdch:id "7c2fbcc8-56e0-508a-84f8-97fb3ad6a8ab" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4722_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CN-6011_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Gum" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "60c8633c-16f9-4066-8aad-311b04b935e5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "4d620a8e-517e-43b2-ad44-d9a8467e73a7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6e767fc9-0f5a-49ec-999a-cda2daeba6ff" ; + crdch:id "afbf3020-1715-4e74-8224-05e316796999" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "47e7b839-bde5-4b66-98da-7ed6e3e7c29b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "83b525ab-ad48-45fe-bbe9-54d6ce88054a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9e74f3f5-ab22-55d9-a79e-9884f3b0f109" ; + crdch:id "de41284b-65f5-592e-99bb-9157a9509c36" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5374_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-T3-A92M_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; @@ -7078,72 +6385,75 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "88000b86-9334-41ef-847d-6668d17ec62b" ; + crdch:id "cdefaeb2-3a2b-4094-b25e-0c509b62c13b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "27fb0ae5-d8a1-46ac-ad3e-2464c52d9cfd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "d22843cb-8a14-4592-b339-a04cf1514205" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "617df1e0-b075-4610-b6d5-8850786fea70" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "86c72a0c-24c8-4d55-9f87-6b7198a10890" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -7154,20 +6464,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3c0d1fbc-508c-4cad-a9eb-a848fc20ac76" ; + crdch:id "af6475d1-2529-4772-9e9e-ce83e3dc0cf8" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006868-2957_diagnosis" ] ; + crdch:value "GENIE-DFCI-008645-7086_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "abf5cf5e-2352-4ba7-9a91-cbefe78ae28e" ; + crdch:id "30b0ff9c-3106-4ce0-8657-3ed59c1c8fc7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -7181,177 +6491,85 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e61558f0-d90a-5bd0-8485-ba159dba3010" ; + crdch:id "a08be31b-24b0-5fb3-b49d-955fcce7603c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-7862_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-D6-6827_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Lip" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a61be572-405b-4b16-b554-7fa6c12a48a4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "460e7821-2712-4d74-b5a1-b2883b3197ca" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "091478b2-f8c5-4ad8-9c89-06a48728fa2d" ; + crdch:id "c53d6135-c614-45f4-8f41-49b20ed4a549" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fbf59d12-7047-49b1-9002-00030c797438" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "2ef80e58-961d-45d6-ac3a-a520be3728c9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d234a346-038c-58a0-824d-22bfabb73218" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-MT-A51W_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "03c6ac2c-c6b6-4041-a024-f2556fab62b8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "91e56a17-b4e8-4ef7-b587-a83bcd8c062d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d238e52b-b2e8-479e-b76c-a168136e0ef0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; crdch:text "stage i" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ] ] . @@ -7359,20 +6577,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "22080645-9bd1-4303-ae61-8228c254dc24" ; + crdch:id "80571628-74cc-4067-b16e-40cc5b040560" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002746-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0020147-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-02T20:58:03.565619-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c74deddd-6181-4108-baf3-4d750d877606" ; + crdch:id "10e9e747-568c-4276-9275-1f1d7cb30f81" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -7383,50 +6601,23 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "08272717-6b2b-4734-9674-4bec2662bd32" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-UHN-523097-ARC1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "ffef8dac-d99c-4426-ad9e-f4e3947fe1c1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f0cdd17d-5db9-4c58-84f5-f9efcc94dcb5" ; + crdch:id "10fdde54-4aab-4498-925c-38ccd8df431d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0004492-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0015591-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d74d27e4-88e8-4ce3-a1ff-7658e007a49a" ; + crdch:id "d2928928-ad9f-46d3-89a5-a00131eaec79" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -7437,110 +6628,218 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "dd691506-83cb-50c1-ae0a-2583d57079d3" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "98a4badd-be86-5ac9-b0d9-9099d5bdcdef" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A499_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CV-7247_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9ca906ce-18f9-41c5-afcc-353b26fdebaa" ; + crdch:id "f84ae44b-4bb7-4841-aee0-139cd79b9680" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "13da732f-058d-4635-a2f0-81e73c725b8d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7d93ba42-9e87-4a6c-8b0d-6f185645a90a" ; + crdch:id "2e9cdad5-53ec-4b5e-8a1e-4f8abee04149" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5ec51826-98c1-49d2-a990-7a95ee636753" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "stage iii" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6459d972-a02b-5a11-a7ef-12f699047036" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CR-5248_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "0771e98b-4e65-450d-afc2-33d4e30b3df2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a4dca71f-e53a-4bd0-9d1b-3381ed188a41" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage ii" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "523155c1-e181-4d6f-9873-9449a8e3c289" ; + crdch:id "5c73649d-f112-401e-a47c-785337555930" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-036955-74886_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-JHU-02535-03020_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T23:09:11.890404-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d34c6f0f-6b69-4820-8dc8-90d8d54ff7c4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "552900c2-144c-4340-aed9-197382fafed4" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD17916_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:57:41.511744-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9ed6f000-4643-4f65-be84-8fd380d3bc36" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "d4c804df-7392-4267-908e-8fe8c37d00cd" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -7548,70 +6847,73 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f6106a03-d94d-5b31-969b-ddd1d6ac23f7" ; + crdch:text "Basaloid squamous cell carcinoma" ] ; + crdch:id "f4e541cc-a71e-55b3-ad08-3eeb8d00f2b0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-8596_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-KU-A66S_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8083/3" ] ; crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b8077f12-81e6-49f1-aa69-a4b6f5825534" ; + crdch:id "3c09f5ba-a4af-4384-948a-d6e943613f7a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "226992b4-f81f-49f5-a1da-37ab1742779b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "4bed3ece-2350-4c99-bec9-3d652fbe8c9b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "51eeba12-4cfb-4842-ad6c-e49cfe5ef207" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "a590a632-55b4-4be6-b2d8-6c8afbbe99ac" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "stage iii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; @@ -7621,117 +6923,93 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "T2" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Basaloid squamous cell carcinoma" ] ; - crdch:id "fb148e0b-2d1c-57ff-acd6-4f2208af3ce3" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "5b91d8ab-6ed3-4c0a-a56b-8f0e151eaf5a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A4IH_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-000195-4559_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8083/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f87efb5e-24f5-4d2b-b6b3-987bbda30e03" ; + crdch:id "52beca45-8506-41fa-b0a0-3a8c24c9d7fe" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "3adce70b-ce30-4b21-beeb-2a7bda73ca3d" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-008134-5168_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "eff60f0d-e3c1-4a93-9026-c0764c70ba9f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Not Reported" ] ; + crdch:id "37b86231-4224-4084-a523-800e98c4fea3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "6fdb9066-4bcf-42aa-81d1-585b2f2fdaf9" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6579daca-0ec7-49e8-92e5-6a6b7c379b8d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-6209-17288_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-GRCC-h39utsgs-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T18:19:50.810302-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0f97f0c0-2148-4c06-97a5-37a64ed1b81d" ; + crdch:id "1f1c82de-2931-4f38-9caf-213d5425ded1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -7745,41 +7023,57 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6ce57628-3cd7-5cfd-8317-cadf76a37f43" ; + crdch:id "ad86791e-dc2b-4a82-9c74-674bc6baf268" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-7870_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-009352-7151_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5e386079-a9c2-4c7e-80ed-9dda270249b9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "a71bc3c7-5807-5766-8487-c3dbc27484cb" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CR-5243_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0d53784e-011f-4890-9cf5-59e955dd1fea" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f5589c89-0b94-4492-8a3c-84d58377e94f" ; + crdch:id "d89d46ea-9a7a-4fd8-b11e-9c9ca4780119" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b79164b1-7abb-4585-b23a-0e610734ea8b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "6fc08372-0d9d-4b3c-b656-9573fa532c99" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; @@ -7791,60 +7085,54 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d670dce6-9fa8-402a-8b79-081ec26ebe25" ; + crdch:id "4c9f5000-dbac-4497-b434-57036c18a022" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-000843-6962_diagnosis" ] ; + crdch:value "GENIE-DFCI-008669-7093_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "85fa5941-b6df-4eea-97e1-a7b4ae310bdb" ; + crdch:id "c0927894-b73f-4930-b147-e079caeb60e5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -7858,20 +7146,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "af2c06c6-b5cb-4369-906f-727e8e00e459" ; + crdch:id "c1111640-7729-436a-9b46-88c0ab534b96" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005169-1136_diagnosis" ] ; + crdch:value "GENIE-GRCC-832679ee-sample-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "104530ac-b606-41bc-93e4-5734f176d3bb" ; + crdch:id "9590434b-5b17-4ee8-b109-7ebb737252ef" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -7885,202 +7173,107 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3f9675d2-ad2f-5a88-af81-e7e9b5744c1a" ; + crdch:id "3f296a63-9ea9-4648-a621-c8fe8a6d631e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7437_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-GRCC-cbxznf5u-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "215c17d6-2035-48da-9d06-c54734042898" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "58c15c00-ddad-4f65-9f03-1882b7f9a09b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "46be59da-3e8e-43cb-a4f4-6658b12f1fe9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d7340d97-4ebd-4125-961a-9a5abe2f0ebb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "e0559edf-8fa9-43f1-acbb-7964ea0c33d3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3ef5f7db-6234-5c11-96d5-fdb6cf8ad63e" ; + crdch:id "155420b6-0bc4-42f0-a28d-863e56f9e200" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5978_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD864_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:58.520537-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b33eba98-6a89-4454-9a53-94999cd5003c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "24318871-5bfe-4bbe-8df8-9e415558ae47" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b801368a-b10a-4a42-bda8-5df8216b532f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "1fe06c82-aa43-44ac-a091-8dec17e796ba" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-037687-158970_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:26:11.717995-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7560ec6d-e0f2-4b55-88bf-62e7173126a1" ; + crdch:id "98e2382a-2d7b-445d-83ff-1dc53d66db12" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; - crdch:system "GDC" ] ; - crdch:text "N3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N3" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1ad86ae6-e1df-4578-9639-e768e6711e61" ; + crdch:id "89e61c6e-3fb5-494b-81b3-7280119fefc9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008033-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-011185-11116_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "28cb9e1d-c34b-4909-a387-5a5c60bcd6e3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "25bebf87-88d5-4cd5-b2d7-3f2b7c1a0a02" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -8088,207 +7281,104 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4d192f26-a2c4-537b-b8b5-1473a759882c" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "6252ba82-08cf-4a88-892e-bd2847842225" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A7J9_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0009588-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5df6c457-baef-451d-b1cf-eb7fa6adc602" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "0fd4a1fd-2313-475e-ae01-d424516e42c9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "6f840d0f-a369-413c-baf1-35200313c274" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-a679ee35-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5be42d60-80c3-486f-8717-801fec0c89d3" ; + crdch:id "60e15dc9-5d8b-4104-b6c3-bc0b7b3109a5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "fbceb407-e7f8-4942-8689-854f8999672c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1214a9ed-2d43-50a7-9a94-85eaa002670b" ; + crdch:id "36009b16-600e-42f9-9509-783c76c5b88d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A6DA_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-034499-159099_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "33bf2824-d873-442f-8ae6-48274fbf4a94" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "a2260bc1-8aa1-442c-933e-e4a05d46d802" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "8b80b922-b00f-4cda-92a2-49c357aea89d" ; + crdch:id "bce047a2-b5b7-4ccf-8bf9-406d8c87d7a3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "38c088b1-bab2-4d5c-8f45-80280d1c309b" ; + crdch:id "e7fe03ad-184c-46be-adcb-dcfc79db3492" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010800-9387_diagnosis" ] ; + crdch:value "GENIE-GRCC-d47c6375-sample-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b480938b-4562-4d37-a280-16cd4dc700ca" ; + crdch:id "7512ff60-162b-41b7-a3ed-c153d7aee073" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -8299,418 +7389,344 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c127a1e6-f25a-525b-949d-013bac98b38a" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "20b2ca7d-bce3-44c1-a0db-ef271aca97bc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-DQ-5629_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD2717_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:58:58.753780-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "57ea3eed-f8e2-4310-90c0-50d89f818a12" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "69907c44-c952-482a-a307-44efd82a16dd" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "675831ed-0976-4fdb-87da-15a7a85ba6b5" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-9bb5e551-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cb2da33c-021a-4af5-8509-118bc1e8e0d5" ; + crdch:id "b2ee3f62-a9d8-4f49-bc51-1d3f17d63b14" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "769f3c1c-323e-4f04-9ae7-e41f484a964c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "812129f0-3b47-5ede-9062-237e0c0be7c5" ; + crdch:id "22e091bf-8af8-5910-9664-c73e7b5f44fb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-5555_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-6487_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "99ca3c12-0d63-428f-8b1b-03e4a3e8e233" ; + crdch:id "ff63290d-0644-4387-99bb-697150a7fb6b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7c56b9e6-8fd8-4d39-92f0-a24c80270dda" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2920ca1c-6035-4350-ada4-c60d485dbfff" ; + crdch:id "027dedd3-bd53-420e-b7f2-eb5b8c26bcdc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "stage i" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9e30aa6c-91e6-5dd3-9512-75c162a89913" ; + crdch:id "39fa27e5-b36f-50e5-b173-1bb73a1ba5ba" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A8Z8_diagnosis" ] ; + crdch:value "TCGA-D6-6826_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1efb2d28-ac51-4d70-a24d-667a2b53467a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "a31ecf7e-1838-412b-ac34-6fd8810739c9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cff6967e-e8f7-4a25-aa31-9328e4b42816" ; + crdch:id "1737989d-8463-4761-b111-53e4fd396375" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a118da56-784d-4b67-aade-d9a7a8b49f18" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "7aa13049-917a-4d7a-bceb-3c718ec8fb7a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVC" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; - crdch:system "GDC" ] ; - crdch:text "M1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; - crdch:system "GDC" ] ; - crdch:text "stage ivc" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVC" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "N2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M1" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f8933756-4001-4c7b-94c7-2d8964ffda9e" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005118-1198_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "430338db-7df9-43c8-be80-6ef5a6b98899" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "27b201c5-0310-4f7a-835c-31fde311cde6" ; + crdch:id "da5ce97d-de12-5384-a88d-a9874b39b7dc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0020040-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-QK-A64Z_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Palate" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-02T20:58:03.565619-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8738d7cc-e80c-4a00-bc4e-fee451f4b19f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "95525590-0eea-4017-be66-dc487b78299c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bf8ae40c-068c-44c4-b09e-954969e83369" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0016039-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:text "Not Reported" ] ; + crdch:id "67289d96-8140-4ba1-9863-124950488c1d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ab79d569-bc64-4639-a6a8-74bc2bbe0d0c" ; + crdch:id "eb25346e-0e28-4161-94c8-916b41f8d969" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b5b027c4-6ae8-4c42-9ffc-46738ec336b9" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-671452-unk-1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:05:42.341898-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "eddc8197-6d13-4eef-bb1d-06d1b8df5395" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "6f1ab30c-67b7-4a7f-b4ef-22b1221bec7d" ; + crdch:id "c9269eb1-ab75-4719-8cd9-e9efd32f7d7e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0012422-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-MDA-5245-16353_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:17:29.664139-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e125a436-ca27-4a85-bd9d-9ca108306229" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "05d9d8f7-c21d-47ea-bb12-7de5f6709096" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD14142_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:42:51.054806-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "02402659-6c66-46ca-861c-e4c093a1a3d3" ; + crdch:id "08209047-3b7a-4295-90b0-ddc92aa1e1c9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -8722,23 +7738,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cb8fb063-f8b5-4748-b937-5efb6fefecfc" ; + crdch:id "ca8d9936-f4d9-465a-8640-66a91f735a60" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004149-1026_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0018419-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:39:49.045696-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e331b564-d79c-446d-bff2-a732dacba6bb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "60efb1a2-a8b1-40a7-b230-e4b532a8048b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -8749,12 +7765,12 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b4c405c4-ece9-4cd9-b11c-cb1f863021cb" ; + crdch:id "12b8aa2a-5f0f-4d64-9cc0-ff4a65619c10" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003788-772_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-003438-7875_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; @@ -8762,7 +7778,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f933f399-d986-43eb-bdc0-b3faf49bf513" ; + crdch:id "8ccd1ad3-a277-468d-ae44-03e6c1964c3d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -8776,185 +7792,130 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fac833bd-36d8-5306-b322-92106575bfe1" ; + crdch:id "0a622048-699a-55f4-ba31-6c9e95e1cabd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5430_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-DQ-7590_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5bae7161-8838-4b10-9210-02deaae4b9c1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "b8eb9edb-fce8-4e72-9cbf-c4868c04965c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4151c76f-9dcb-4451-a99b-889e0024f8b9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "72f98dc0-3fcb-47a4-8c7a-52a7cd9d3fdf" ; + crdch:id "36fb3f52-714b-4b86-a7a5-ca4b017fd182" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5d293d68-61ae-49ad-bfcc-e0bdb91cc29e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "95018dba-f23d-4af0-b774-c28be60007f7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; - crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "TX" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6459d972-a02b-5a11-a7ef-12f699047036" ; + crdch:id "c0bc6849-2b35-4465-9d65-38c3a21a9a25" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-5248_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-MSK-P-0019226-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "a4dca71f-e53a-4bd0-9d1b-3381ed188a41" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:42:00.849990-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0771e98b-4e65-450d-afc2-33d4e30b3df2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b33d58a0-8855-42ac-baaa-0a1e961307f4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "d75594bb-d5e3-496f-b1c9-1743ae942c53" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "bad7f79b-abec-4d69-8c30-3abd1a5f31d9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008027-5967_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-UHN-700007-ARC1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:21:56.842750-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f0afc508-eff1-4a28-b912-3705a87d607d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "72155863-300c-4515-962a-d0c332cf5b63" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -8965,91 +7926,80 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "20846d6c-1a34-5e01-a531-f9c783416c3e" ; + crdch:id "0c55f80d-c82c-4554-916f-6b117978b3fc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-MZ-A6I9_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0000454-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0551272d-7e05-435c-92b3-918cde4d14ee" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "5c3a5e81-481c-430b-9c70-f2d61a77568d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "396f116a-bede-472e-847d-435a77dfa7dc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6b76278a-cb58-4308-bfef-fa1902a02375" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-010467-10870_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f32ce523-c60e-4a86-bfa0-eeb4f3b2d83a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "02cf8f79-3109-423e-b290-9b0cf112e827" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "82cf8f30-edc0-444a-9607-498f1f4fc6a5" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "05d9d8f7-c21d-47ea-bb12-7de5f6709096" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-NKI-ETWO-SK3U_diagnosis" ] ; + crdch:value "AD14142_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:42:51.054806-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "92e24628-56bc-4c65-9c4b-76c589943948" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "02402659-6c66-46ca-861c-e4c093a1a3d3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9060,9 +8010,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "556216dd-a648-5f7e-a4b1-8f8688a354b6" ; + crdch:id "7c0c3290-5b41-50b4-b37d-536ebbac2af8" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-4217_diagnosis" ] ; + crdch:value "TCGA-CV-7101_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -9072,89 +8022,117 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5eacbcc3-8ac1-42bc-b3dd-53bc693d3cae" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "397b08f6-f560-418b-a6e6-2d953187bd5d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b9427fad-04aa-4e73-99ba-ccde04e4978b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "8e461b7f-1bfd-476d-a948-7aadb89a41e5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3d9307b9-f42f-421b-bebe-ed692a5868ce" ; + crdch:id "79ec5357-3a44-40db-a1ba-ee282b484526" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f040a5a4-e955-4e69-9f2e-ae9a4c78780a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], + crdch:text "stage ii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "T2" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "1906d9ae-58dd-4b92-892f-6ff61788d171" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-005398-2604_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "adbb22ae-5402-4918-a4d0-b54e2f114253" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "7c9e489a-67bb-5aef-92cb-b776ab07f413" ; + crdch:id "b62e9fa2-da66-5eb2-b390-96985bc92b6b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-A6EQ_diagnosis" ] ; + crdch:value "TCGA-H7-A6C5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -9165,102 +8143,112 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "37e8e5f5-0edb-420a-9f32-a2e167ef4cf4" ; + crdch:id "069b94fd-00fe-4073-bfca-3a3a8057d1f8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "041d7de0-fdee-4f6b-9945-058f8bab509c" ; + crdch:id "875069b7-9411-4fb1-b8a2-992a052bee49" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "43a91c60-f1f5-4b10-b0ee-c55afadac481" ; + crdch:id "9b557922-d796-48bd-b194-1fba8622f254" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "578cf44a-2d2c-416d-a428-69547378bb9b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "60a003d8-42fa-4981-8fa8-a96a6f4205ad" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "426ed511-e284-4ddd-9809-312805a88905" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0019316-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "AD3816_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:43:52.092583-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:01:59.757092-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b3eb534b-6441-4294-809a-ab6963d9aa39" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3fa16cbf-829f-4097-ac9f-d8016c40c618" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9271,74 +8259,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3f8fca8c-e8c8-4032-a0ac-488e49fd623d" ; + crdch:id "7bbdbf5a-baf7-55b4-bd8d-89e213744a26" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-023359-23864_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-QK-A6VC_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "76240522-a39e-48c7-80e0-241277fdb705" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9eb7cb20-106f-4668-9ef4-c0344e8df3c1" ; + crdch:id "d278f388-2a5f-407f-886d-961272ca28eb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "dbea2268-ac62-4ab7-aa7d-86f029fcb2df" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0722d8c6-5481-4736-a9ea-24253edffa93" ; + crdch:id "cbfef8ff-181a-4048-a571-f78fd34799ef" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005284-2016_diagnosis" ] ; + crdch:value "GENIE-DFCI-037220-88689_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f02ce49d-85b8-4704-9dbb-8e012090fbd5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "8d28ba70-052a-42c0-9a4e-f06ea143f381" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001195-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b857d450-dfaf-4407-84e8-d3bbf843cbc3" ; + crdch:id "9f95c03c-4c29-47c7-8bff-47c3014a61b5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -9352,20 +8378,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "fac35228-e5eb-403f-a9fd-c88a2518c7c1" ; + crdch:id "1674c3b2-c0b1-4395-9822-81016a649ad8" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009544-8452_diagnosis" ] ; + crdch:value "GENIE-MDA-4664-11636_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "933ddbda-c8bb-4e81-9342-9d7379bd6332" ; + crdch:id "2bd6f2fa-881f-4287-a616-d43d33a5e551" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -9379,116 +8405,50 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "31489596-1797-567e-814f-ec85278ee342" ; + crdch:id "eaa3ca60-5565-429d-8c4b-a0a6ef7d9fa6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5432_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-003114-1605_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c552cf29-896d-4a47-8022-e5c57e27e70e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "3a13692e-cb77-464a-8ace-cba47f99247f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "418aadda-9f2f-43be-b171-866585aab114" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b4a36114-80d3-4f28-b85a-077dc31eb485" ; + crdch:id "9e503ae6-5765-4fe6-9a28-eac5a3a93a13" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "100193fa-11a9-4abd-9bcb-b1688eefaf5e" ; + crdch:id "3d039654-a9ad-4641-b459-bd7ccd1ec1b6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008981-6260_diagnosis" ] ; + crdch:value "GENIE-NKI-MCU4-LAZM_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-29T19:51:14.064673-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8fe03287-0b1e-4750-9006-58059562a243" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b34b2488-73cb-480c-a1ac-c2ef5b89c5f0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9499,118 +8459,50 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "de41284b-65f5-592e-99bb-9157a9509c36" ; + crdch:id "22080645-9bd1-4303-ae61-8228c254dc24" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-T3-A92M_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0002746-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d22843cb-8a14-4592-b339-a04cf1514205" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cdefaeb2-3a2b-4094-b25e-0c509b62c13b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "86c72a0c-24c8-4d55-9f87-6b7198a10890" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "c74deddd-6181-4108-baf3-4d750d877606" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Adenocarcinoma, NOS" ] ; - crdch:id "78daf8d2-f74b-4d9e-9ffe-79e90425ad3c" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "509526cc-f60a-4e6d-8a18-2f76ba8e995c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD7638_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0000586-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8140/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:47:53.195932-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a4ae0499-714f-4d0b-95b5-e085bb652117" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "6d54051a-c75c-40e6-9215-3e470f0d242e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9621,125 +8513,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "52d5ae11-4bb0-53aa-bff7-31190888f8ff" ; + crdch:id "eb8958ba-0798-5ab3-b4f4-258d441d7e03" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-5247_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-P3-A6T5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Gum" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "950233c0-c1ca-4b69-8e3f-a6072dbc7e6a" ; + crdch:id "c98f1b7e-5d3c-4e07-9d9c-65c5a6ac6cd6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "43739161-8083-4740-a670-1a334a87ca7e" ; + crdch:id "e45c81dc-4143-4e97-8212-85032c760221" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7fddfc05-49ef-4ebc-8572-05059a5fc363" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T4" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "d2578ad3-da53-4f9a-a3b7-043e9c01a282" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD17065_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:54:42.853523-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c84c230b-7953-4d86-ba93-255ab2242ce7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "MX" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "efe7297e-9961-4ac3-b247-a9322e18240c" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "bf8ae40c-068c-44c4-b09e-954969e83369" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD16071_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0016039-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:38.104730-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "542b7dd6-20ad-4719-bece-768060ddab97" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "ab79d569-bc64-4639-a6a8-74bc2bbe0d0c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9750,26 +8629,19 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1d13cc0a-da04-5925-8930-693f09cd6432" ; + crdch:id "18d9c548-2f10-5116-bf59-05cc53b3b5c6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-T2-A6X0_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CV-7410_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a4b8631d-80aa-4665-86b4-0caa7241da66" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0416608e-19db-43b8-ac11-87406b0164d0" ; + crdch:id "843ced6e-a9be-48ea-9313-13aa752dbbe1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -9777,56 +8649,75 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6f085b6d-6abf-4d89-a17a-89e6c7f8fcc2" ; + crdch:id "acd6cfc3-412b-4f61-a2c7-013c61fa2efe" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a24e0ad7-668e-4bc7-ae3a-94964278a407" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "stage iii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f41a7343-e52e-5f4b-b902-ccd3275b00b9" ; + crdch:id "d957f533-9896-5f0b-a9ee-90335d733f67" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-DQ-7589_diagnosis" ] ; + crdch:value "TCGA-BB-7864_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -9836,14 +8727,14 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e22036a1-ed2f-44b4-8bca-bd9808611fd0" ; + crdch:id "4775330f-0409-4bb2-a096-a3d1eb0180d1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "19c44a45-4f80-4d5a-beac-83db256a3434" ; + crdch:id "f3c568ae-ad12-4155-a652-8e16e5276bda" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -9851,7 +8742,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "41ec6e82-6bcd-4057-a370-bfe1801e2e94" ; + crdch:id "1477b393-8acf-4550-86a7-6570c0d7d583" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -9861,96 +8752,72 @@ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "M1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage IVC" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "491f9f68-fb39-4d17-a75d-90d14e801df2" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD15095_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:44:57.662014-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "ae6cd26b-98b2-46a9-917b-cecd94358907" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "75ebf700-6ff1-4980-a420-41df37dd2c42" ; + crdch:id "c4b50b5a-dee5-481b-8c34-5584abba267f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0018608-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-UHN-614933-ARC1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:39:49.045696-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e4d9ec72-9281-4b2e-841d-06d84634968d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "09f9d0e6-10af-4224-a875-8d1e99e90eb5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9958,26 +8825,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bcef8cad-3d18-4cd2-b839-5fddd16311f1" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "6759d804-a7db-43ed-a3ae-db633fdc7cdb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000945-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0010241-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2ba57cf3-fd06-4f99-9ad7-447a164b9586" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "856fab11-14d9-4e8c-af8a-65684ca39418" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -9988,23 +8855,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bad7f79b-abec-4d69-8c30-3abd1a5f31d9" ; + crdch:id "59474381-516a-4be2-8b74-7fe5804ec371" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-UHN-700007-ARC1_diagnosis" ] ; + crdch:value "GENIE-DFCI-003795-3691_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:21:56.842750-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "72155863-300c-4515-962a-d0c332cf5b63" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "8212fb32-9c81-4bf1-ab6b-337196acdf90" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10015,23 +8882,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b0f16df9-9556-4ff1-b8b8-afabece2fd14" ; + crdch:id "4a315682-7cd0-4c42-9fd0-50ec841a059f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-UHN-071596-ARC1_diagnosis" ] ; + crdch:value "GENIE-DFCI-004723-1663_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5cdc6f40-9b5f-4dc0-9082-a9500c3e5af4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "1291884d-38d8-49cf-b16e-aeab69d83681" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10042,192 +8909,106 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7c2fbcc8-56e0-508a-84f8-97fb3ad6a8ab" ; + crdch:id "812129f0-3b47-5ede-9062-237e0c0be7c5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6011_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "TCGA-BA-5555_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "afbf3020-1715-4e74-8224-05e316796999" ; + crdch:id "7c56b9e6-8fd8-4d39-92f0-a24c80270dda" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4d620a8e-517e-43b2-ad44-d9a8467e73a7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "2920ca1c-6035-4350-ada4-c60d485dbfff" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "83b525ab-ad48-45fe-bbe9-54d6ce88054a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "99ca3c12-0d63-428f-8b1b-03e4a3e8e233" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "388e26e6-e8e6-527b-929e-24ff75edc9b4" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5441_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b480eb37-ffe0-4626-b49d-dfc514a60886" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "26c67c48-00d3-4491-b761-7941415a2c6f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "3f583e59-c92a-4257-8098-5d081642dea7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "530535a6-b47e-48ce-b312-54c3003c14ad" ; + crdch:id "23193585-2a17-41cb-b577-8044058658ea" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002854-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-8k5ygy35-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ad472d22-bccd-401b-ab2d-0ab7a31c7b73" ; + crdch:id "5db1c5e8-ddbb-4057-a059-6acf46826258" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -10241,23 +9022,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d113feec-68eb-4294-b6b4-6b8e22ce56bb" ; + crdch:id "1dc5e826-3f32-4d4d-8e2c-00fdbd76b393" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0016562-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0010503-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:49:52.836213-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "99c1a34d-ba04-462f-be28-bb5eac77b316" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "78c3f61a-5719-4604-8ebe-c21057d3e416" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10265,110 +9046,234 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "1674c3b2-c0b1-4395-9822-81016a649ad8" ; + crdch:text "Malignant rhabdoid tumor" ] ; + crdch:id "d1368e23-4a00-5b0c-ad28-56a5a4dbd833" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-4664-11636_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TARGET-52-PATYUA_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; + crdch:text "8963/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2bd6f2fa-881f-4287-a616-d43d33a5e551" ; + crdch:id "83a37c0f-ac29-558c-b7dc-a9fcfed82b61" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "unknown" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9be1751f-17dd-5748-a489-1b4eb3235e17" ; + crdch:id "706b1290-3a85-54ea-a123-e8bd14b085bc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-MZ-A5BI_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CN-6012_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c226c7c5-64e6-4790-a420-c2f4e0196453" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "e23c7006-1a13-4211-8920-47548641e574" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f1e46036-7b4f-4cca-a150-f2d8e599fdf7" ; + crdch:id "8b2588c8-4261-492b-b173-2490a5de668f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "badeaed0-2625-4a4d-bb95-d295e2c32c01" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; + crdch:system "GDC" ] ; + crdch:text "Basaloid squamous cell carcinoma" ] ; + crdch:id "35c83c03-b2ab-5f6b-a231-66a3f879a217" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-P3-A5Q5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:system "GDC" ] ; + crdch:text "8083/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3b3502ab-ab9f-49d7-be08-243a7022463f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "2e1b4cf3-61fe-452c-b800-f9bc53333713" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3f5cd265-0dd3-40c3-94b8-e92d18ce87b0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "be59114f-e2eb-4d06-824e-7aa867673eda" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "96053970-fb5c-4b79-b1bd-8eb8690def1c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004755-1862_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD1118_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:12.328231-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "255bbe44-dce0-4905-86bb-317144348172" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "8f636ed2-41a2-4c3d-bee5-40d9755bf674" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10376,26 +9281,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2a826dce-5a83-46e6-8ff0-9c7597ff54d4" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "d50387b2-938c-480c-8287-6c8754e06278" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-673077-unk-1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MDA-6686-17868_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:05:42.341898-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a5fa104a-bb1e-4e7d-a740-607fc803f4f3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "2022f8c2-108a-4919-bbcf-1dd1ba4fa10b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10406,20 +9311,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "c740d9c9-bb4f-4ae0-9920-43267c9bc180" ; + crdch:id "0e8b9b8f-041a-4d83-8af0-503b7d84e00a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD14561_diagnosis" ] ; + crdch:value "AD4383_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:42:22.825295-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:07:26.436903-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "97cac184-023d-4aaf-9637-cc34969471cb" ; + crdch:id "ea5776ba-c4cc-4d4b-9e33-573ea824853a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -10436,23 +9341,86 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "8bd7b118-92b1-4443-8753-f779c82ef116" ; + crdch:id "64881717-bcb2-532a-b0af-395ba5c62c2e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-035615-74950_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-6481_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-27T19:26:40.896040-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "151f2c1e-f448-4fa5-9b61-81dc5c339f58" ; + crdch:id "04652163-a674-446f-9e86-607de19e4c34" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e9a39a90-6401-4a9f-baa5-606e8b5176f6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "b03c5a4b-9dd8-4186-b8d5-a65acb317474" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD3459_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:04:01.286185-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "c54fca3a-3919-4ac7-81b6-f1cf955f47a7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10463,23 +9431,26 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e7fe03ad-184c-46be-adcb-dcfc79db3492" ; + crdch:id "acb41bec-39c8-477f-8cc2-b8c982bf5b2a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-d47c6375-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD9755_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:57:54.983619-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7512ff60-162b-41b7-a3ed-c153d7aee073" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "2b14983f-b848-45de-9881-5dc4f483f7a4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -10490,524 +9461,411 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c2494ea4-5db2-5716-9afd-096e152b592c" ; + crdch:id "37b4b703-52d6-51dd-9cd7-3f759862a78c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5356_diagnosis" ] ; + crdch:value "TCGA-CN-A63W_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fb9d2ba0-7673-4587-ab69-0059fce2f671" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "e6cd0e23-4423-4ebb-b314-913419340811" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bcb5da85-78d6-4519-9740-378587b1bd37" ; + crdch:id "9b9dbf11-d017-4723-a76f-c25ce4a01f09" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cf684788-d8e6-49da-8421-b2dbf040a529" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "8da610b4-0a32-4ef8-9f55-1c969addd79f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "92f6368e-51fb-56bf-a72d-7ccc16eafb44" ; + crdch:text "Adenocarcinoma, NOS" ] ; + crdch:id "1c3027a0-7ae3-4ee6-a71d-b357ad841b3c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5434_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD4542_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "657cf588-cca0-44c2-83b3-0e87f7a81f29" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8140/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:20.797099-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3f70e2db-b313-4f3f-89e7-cd1c0acecf9b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "de90601b-1eda-4d1a-aa41-29feebdcfd57" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "dc649d39-482d-4855-b9e3-129552e5e421" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "65645e51-3cea-4c45-a029-ecd7cef6c8ad" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-001639-6186_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f6130e55-1627-4d2f-bd8f-c0e778a1aa45" ; + crdch:id "b1a851b3-94bf-4652-82d3-cc6133cd1565" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "48994484-82cc-51ba-a8b6-6f4663599d40" ; + crdch:id "0099f9fb-0d9a-46a0-a86f-c10dd58ad440" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6478_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "AD8066_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:17.672127-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a26d04d0-1501-4cc7-afea-154a89cff0ff" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "dc97ccf6-b026-45ac-a658-fb44806230a1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Adenocarcinoma, NOS" ] ; + crdch:id "215314e4-f8c7-47e1-8993-f126c49bd1a8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD7896_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; + crdch:system "GDC" ] ; + crdch:text "8140/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:49:07.730023-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "dfbc5ddf-a361-4d72-ba8d-5615ca644357" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "d3811cf5-8f54-4344-9efc-2f42c49e4e67" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cf93d012-b0b8-57b3-8a55-7575dfde2b1d" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "faf259c7-d577-5ef8-9075-9a42f1083260" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6989_diagnosis" ] ; + crdch:value "TCGA-F7-A622_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8071/3" ] ; crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a5c6b30f-2aa3-48bd-8415-bdce2444e49d" ; + crdch:id "32d7cb3d-5f5a-474a-9dcc-3b5f2dc64d22" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3570ac4b-b585-4262-b54b-137a2515c689" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "32056265-c5fb-4544-9f99-22b34febb805" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7ac8fb22-0a09-4b16-af8c-b5c2e90a968a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3901d8b6-f2f2-45e9-a40f-3ccd679f701e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "52fd0265-204c-4ce3-bb51-a3cbee5aca51" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-115ef99e-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "6ba7ff9a-775d-4239-884f-4a303b42e4fd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f14b2d60-39ff-428e-bfb9-a33f4d3242ee" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002193-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f2f48558-d331-431f-a14d-845efe0c6ce9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iii" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6bbf8ace-0b17-57e5-bf9e-2c164cb28e53" ; + crdch:id "693a7e67-099e-5382-b7e2-e70d6d15406f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-F7-A50I_diagnosis" ] ; + crdch:value "TCGA-CV-6962_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "384902a7-fa03-4083-9baf-7ce114694c9d" ; + crdch:id "70b5b27d-3905-40de-8b70-9185cfc49d94" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "366f8ab0-ddd8-4383-9bc1-96ef342b749c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ccd8f2ed-5a6a-460f-b692-ee7d78e29b18" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "5b2faa3f-c96e-42c6-81ce-a356852ea6a6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5eb175ff-1b47-463a-8f16-4b59914457bc" ; + crdch:id "73d79c62-61b6-4e72-bc8d-c3fa2a344caf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2b051980-b5b7-4b1d-900c-9705c24b2a78" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009287-6605_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "781e0bea-f234-496c-915c-c163fc8de24b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "430602f6-cd8b-48d1-b519-dee691fc9c20" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003106-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "78b77808-ec88-4e6b-8393-decaa7bba86d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "4228d736-f7fe-4ef9-8bce-39b8c6c3bc70" ; + crdch:id "094085f3-01f3-4992-b559-832c897a704f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010459-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0003374-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d69183b2-2961-45f3-a4db-3d32d08f6abb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "e868826f-a629-4839-bc5f-5383b74aac12" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11018,131 +9876,173 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "881c2131-1f0d-4b11-8b3a-626918ad5566" ; + crdch:id "fc136a78-0ba0-5a79-a4f9-d5d692e61222" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0013652-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-7402_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4c4f2c9b-d2db-42ab-898d-7d6c8c8e4a6e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "826319f7-67b5-481a-998b-781e3ded01c1" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-22f8acca-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:id "dfdf096f-9577-4e8f-8e98-9b808e417ccc" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7aa50a3f-dd6c-496c-89e2-2d8d6d136acf" ; + crdch:id "b86e8a21-6937-4299-89f6-05f51888f5d8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "49cde226-3d69-415f-ad98-02d190dbf75c" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006446-3455_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5c19b5fa-d6eb-4d7e-b617-930e19aea484" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "675831ed-0976-4fdb-87da-15a7a85ba6b5" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "c8cffdf6-7c37-5146-9bff-2cbd5a6f5bbd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-9bb5e551-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-CR-7364_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b2ee3f62-a9d8-4f49-bc51-1d3f17d63b14" ; + crdch:id "6ced7677-159f-4e9f-b550-627ab9ea80f7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a17406af-2eda-4148-8a0d-ec2ae4bd9fac" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "26bc85c7-5376-467d-a880-4c415ba3b3a5" ; + crdch:id "ada2a9ee-43ec-4198-b1e4-bb0c62102973" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0014015-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-003061-9096_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "968b2133-a7b0-4d2f-8949-f6ff299f1219" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "7d368af5-dc58-4ddb-af35-cbc63bd638e4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11153,101 +10053,288 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "57e78d94-5a02-499e-953f-e5539884009b" ; + crdch:id "a66ce9f9-d7d0-5f2e-b0c0-73f306f68236" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-036456-74857_diagnosis" ] ; + crdch:value "TCGA-BA-6869_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-27T19:26:40.896040-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f4ed2c84-39f8-4ab3-8762-a9920acc2432" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-23T13:20:20.149518-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6f3b4fcf-0519-439f-b3e9-6a0678745885" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "2f9729e6-edea-4612-82b3-01251317074a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "0aaa8bba-f4a5-4158-b9b4-a02244b5f6f7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iii" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "e2403080-b7b5-4d13-b62e-9b7293a45058" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "4176108f-948d-5715-afbb-cc21f3cbfaf5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002484-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-CN-5363_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5e4e1e21-8016-4e27-8f72-2411714203e8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "89363cf2-b8d0-48cd-97e5-4cd68ed372d3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "d0161f8c-9c53-47ad-895c-40d1be3a814e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "591e99ec-46f9-442d-ac20-745dccc8a52b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:system "GDC" ] ; + crdch:text "N3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "stage ivb" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:system "GDC" ] ; + crdch:text "N3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0be93ffc-ad62-42bb-892a-ba10c4da6f39" ; + crdch:id "54c68cb3-653c-5035-829e-11c7b3853119" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0017332-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-7089_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:20:07.713564-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "43637316-5d63-491d-b4cd-2caa045d8c7d" ; + crdch:id "7f11de1e-f75d-4476-a179-b50a84a45a78" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f2e436bd-bbc1-4b1d-9a55-e2a83a1bb510" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a6c24a00-67fd-4a1c-a371-b6e387dcea61" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "267e43c1-bf99-430a-b077-147985fb7e64" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ad86791e-dc2b-4a82-9c74-674bc6baf268" ; + crdch:id "e980228b-ecef-406e-91da-09bc06d5ad04" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009352-7151_diagnosis" ] ; + crdch:value "GENIE-DFCI-000968-1363_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5e386079-a9c2-4c7e-80ed-9dda270249b9" ; + crdch:id "37ecc052-0274-45dd-98db-fb0d5476fa16" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -11288,112 +10375,34 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f29e70db-e331-5bcb-82fc-f2e15cad5985" ; + crdch:id "bd3b2bda-4737-50bb-863a-334134a31156" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7433_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-QK-A8ZA_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c2530f39-c334-4a38-b75b-b74d5cb95920" ; + crdch:id "9adfbc71-da3c-4a8e-a72f-76690e90a8ca" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2916fc1e-ba62-4494-8014-dfcc6dd358ea" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5c4960e6-92f7-4576-a7d8-82a7c3d7cd5f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "43cceeb5-008a-58cb-b219-34c3ac43e86f" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A497_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; - crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bea32bd5-4068-4351-994e-09b3bf819ebb" ; + crdch:id "4db7e146-bf2a-4729-ae80-d471370b62a0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "882c6ec3-1f56-43c3-8a41-da060f9f5ee1" ; + crdch:id "f92383bc-5869-44d6-a128-60b60043d778" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; @@ -11406,168 +10415,218 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "54c68cb3-653c-5035-829e-11c7b3853119" ; + crdch:id "d670dce6-9fa8-402a-8b79-081ec26ebe25" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7089_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-000843-6962_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7f11de1e-f75d-4476-a179-b50a84a45a78" ; + crdch:id "85fa5941-b6df-4eea-97e1-a7b4ae310bdb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; + crdch:system "GDC" ] ; + crdch:text "Basaloid squamous cell carcinoma" ] ; + crdch:id "b4c1dd26-92ca-5bf7-b861-bff7f68e8436" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-P3-A6SW_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:system "GDC" ] ; + crdch:text "8083/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f2e436bd-bbc1-4b1d-9a55-e2a83a1bb510" ; + crdch:id "50e494e8-d48a-44ec-91b3-5755b42f70ee" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "267e43c1-bf99-430a-b077-147985fb7e64" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "dc6d258a-dba3-4186-bf89-9efb70a32365" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a6c24a00-67fd-4a1c-a371-b6e387dcea61" ; + crdch:id "0b1a1f48-c58d-447a-be06-1f4e0c1c39d2" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "stage ivb" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ] ] . + crdch:text "N3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; + crdch:system "GDC" ] ; + crdch:text "Malignant rhabdoid tumor" ] ; + crdch:id "cbc897af-ab20-50cf-b397-5bdaeadb4691" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TARGET-52-PASAMZ_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:system "GDC" ] ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:system "GDC" ] ; + crdch:text "8963/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e5a4af40-c272-5aeb-942c-4be4614b4cfd" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; + crdch:system "GDC" ] ; + crdch:text "unknown" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "203f4d20-b796-4745-9bc0-6385c28ff0ba" ; + crdch:id "d2b0be44-b12f-443f-9d48-3e26ea1ed386" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003320-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD7867_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:48:10.807261-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3a006479-c2eb-457a-b0a1-e3faebae25b9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "1fc039e3-94d1-4fe2-9d51-796dce543f9f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11575,26 +10634,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d1841d22-3350-4037-918a-bb399ed85963" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "fc0ee2ab-b738-49c2-b645-4b6851be5e8b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005202-1165_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-49d6a6ea-metastasis-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "97064320-d382-4d87-a302-72490d7577d6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "c63e4630-7bb4-4f01-b9fe-94478000158a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11605,23 +10664,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "26a2438a-f914-4865-9784-a9a47150cb4e" ; + crdch:id "81f6058e-7aef-4ed0-b7c4-a0f1ff8a52b6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010260-9348_diagnosis" ] ; + crdch:value "GENIE-DFCI-036373-130403_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0d696183-2cc4-4f33-9973-04537cb86276" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3b018cb9-12c9-4445-b021-1fc93e0f74c2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11632,105 +10691,49 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5baa4771-eb6d-56d1-821a-33157bf79573" ; + crdch:id "247e1e60-27cf-4f37-9a1c-8db3284dcb56" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-7866_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-008904-6911_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "af5d22cc-87f4-4b91-97bc-7103bc07adcc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "736c3c8c-ff9f-4892-860f-04665a1f344b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "fb5ba525-1658-4f8b-81f8-8d7ec3727773" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Not Reported" ] ; + crdch:id "075795d3-4e6e-4edb-95ee-f4d7ca56b337" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "8c624d17-a588-40ee-9902-ed694d794814" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "59ca6acf-5527-4fa2-8bb2-658029b9c67f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD1281_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-009312-6572_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:02:30.028866-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a1fe6dde-024f-4487-8838-24fda3505cc3" ; + crdch:id "667948dc-d9bd-4813-922b-69468835c551" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -11742,26 +10745,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "56566536-d3a4-4103-bd5b-550ceaad2a6b" ; + crdch:id "a47bda97-0952-47fa-9a6e-277baa8762a9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5017_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-004713-938_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:53.493092-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e2edc535-6fc4-4999-aa4c-932bf58d344e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "cc589138-6e86-49ad-8d76-857543c02842" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11772,92 +10772,50 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fc136a78-0ba0-5a79-a4f9-d5d692e61222" ; + crdch:id "ed6cd70d-8278-4da3-9067-ab74bc051381" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7402_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-007474-4132_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b86e8a21-6937-4299-89f6-05f51888f5d8" ; + crdch:id "7946822e-6d72-4013-8be2-f3ffb0487d65" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "dfdf096f-9577-4e8f-8e98-9b808e417ccc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d5b740be-4c9a-4bec-835a-4cd0b394ded4" ; + crdch:id "e87ea1cc-7728-4592-9eeb-04d09e11660b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006383-3525_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0005082-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1a1294ab-79bf-4e29-b958-cd6c3b25a984" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "f9e5d21f-2ee2-41c2-b864-f43d6a8357aa" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11865,29 +10823,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "fe440219-2351-41cb-a0d1-e22bc73d4aa0" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "9223ac2b-219b-423b-bd4f-5d28e84c8d89" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD941_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-001409-5066_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:46:27.877516-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5e91c356-4431-478f-8033-99442bcdcb95" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "fc3b12ce-4c74-4faa-ad8b-60ddde831901" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -11898,9 +10853,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e792cf88-dfe7-5130-ab9d-df59b3ed1b3b" ; + crdch:id "ce208b92-611f-5ffc-8a6f-b01b91e7b58b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7421_diagnosis" ] ; + crdch:value "TCGA-CR-6474_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -11910,124 +10865,89 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ef81caac-1fdd-43dd-80a3-4e18eb35271e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "40583cb5-46f0-4966-82c7-4149f14581d4" ; + crdch:id "d84c30b6-e217-4b2c-9dc1-16428264378d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6766e43d-12fd-49ba-bdde-c19bb71d329d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "ddad5854-74a2-4db5-94d1-41196a37be5e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "db8fb969-2213-4290-94de-c3680cd314f7" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD16283_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:28.078592-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0d4e791a-4a50-4c58-a8a5-88e5bf4d7c9c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "247e1e60-27cf-4f37-9a1c-8db3284dcb56" ; + crdch:id "0bf30179-24b0-4b0e-856d-7226a72eb3e0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008904-6911_diagnosis" ] ; + crdch:value "GENIE-DFCI-052973-173599_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:20:30.865187-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "075795d3-4e6e-4edb-95ee-f4d7ca56b337" ; + crdch:id "b39fb248-8053-47b7-aa2c-d69335f218ce" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -12041,9 +10961,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ac0363ed-feba-5584-802a-a8bd096fb07c" ; + crdch:id "388e26e6-e8e6-527b-929e-24ff75edc9b4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6022_diagnosis" ] ; + crdch:value "TCGA-CV-5441_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -12053,139 +10973,213 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3b8fd8fb-429a-47ac-8b99-ae42a3fe968d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b480eb37-ffe0-4626-b49d-dfc514a60886" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d452d59e-92ff-46ee-840d-df8a161ca9c5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "3f583e59-c92a-4257-8098-5d081642dea7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "952f71e6-b64c-456d-8d00-45e4118fef96" ; + crdch:id "26c67c48-00d3-4491-b761-7941415a2c6f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "9461c5ae-cbec-5810-b0a6-9644168accb4" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CN-4723_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f4a14404-3545-44fc-953d-e441139e7fda" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "4a485f87-1a73-42ec-af0d-0b6de2b23504" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "4db1536b-23d0-48fb-91f8-248a03f58aa4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "09ac3334-b77e-56e2-a46b-57faf703f1fb" ; + crdch:id "cf19d9da-2868-599e-9281-91b9e064078d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7385_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CR-7374_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d1553b1a-bc1e-4dcf-a273-b3effabe380b" ; + crdch:id "ece42fcc-b771-42af-92c4-39fd74b645c5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4c4a6867-babe-4032-a639-a9b31cdddc6c" ; + crdch:id "77be0d91-0525-439f-bb34-3a0702c81085" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; @@ -12197,20 +11191,74 @@ crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "415b0c86-82b5-46c1-b51b-00e701add732" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-008675-7728_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b1a78f00-1eeb-4c1b-838f-fb8453112c5a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "e1518a49-5ef2-41ca-ac88-edc88e8ec241" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-e8aa0080-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "baf6aa81-4b32-4d7f-8557-5942a0febb91" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3bd2d2d4-7d4a-51f3-bfaf-4153b96110ae" ; + crdch:id "0584ee86-f589-5812-9bad-03855a31693b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5443_diagnosis" ] ; + crdch:value "TCGA-BA-4076_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -12221,85 +11269,76 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f70fece0-2fb1-4d8f-955b-7b9bbfeb9755" ; + crdch:id "5fe1ae56-74a5-44a9-b8d1-7f05a569bb34" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4863312a-043e-418e-812d-2ae2a1f66f29" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "d6f48bb2-379a-448d-b13d-2dfc5da91d0c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "746322c7-fe75-4b9f-9309-93e9cfa4cb5a" ; + crdch:id "fd99fd83-4040-4738-8a5a-e42d36ecfe0e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "NX" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4e06969c-5592-59ad-b006-09cb82ce6cc9" ; + crdch:id "35b1cfb8-bac8-5abb-85dc-1761cd25e90c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-6517_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-P3-A5Q6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; @@ -12307,33 +11346,48 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "53450297-c715-4c54-ad7e-3152a1e16c45" ; + crdch:id "1ac65133-fc2b-4b41-a101-eacd225f71b1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a2dd87a8-e0d1-47c1-a8d1-70b9730aa4ba" ; + crdch:id "73005780-ea15-4353-b6f7-c26865d3f4d0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8c099f45-3fd6-4966-8cdb-ca4b9288b1a2" ; + crdch:id "b929bf9b-34a0-4fa3-9bd5-49f8097c573e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -12346,146 +11400,123 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage III" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "f2f2d6b1-7233-433d-b34f-62a8d4e50b0c" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0015645-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "8a8010f9-2193-4604-9425-da6e5512ebef" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3f0b65d8-182e-57af-87b9-29e59fcdaab4" ; + crdch:id "0722d8c6-5481-4736-a9ea-24253edffa93" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-F7-8298_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-005284-2016_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8f5a4b47-4c69-4295-a576-fd3e558754a5" ; + crdch:id "f02ce49d-85b8-4704-9dbb-8e012090fbd5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "94c71079-a453-4a4c-b52a-ab686bc83b65" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "4f08ca0e-bd9c-425c-9137-a8bc3654ff09" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0004619-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3f2ed4ae-5b71-48d9-b120-4f7bfd4b34c4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; - crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; - crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:id "407047a0-1065-4e67-aee6-a3a66998deb8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4c3c3952-6e85-4fd3-bc05-81c91ce3faef" ; + crdch:id "915d0d2e-63da-4723-909a-4bece5afab90" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003978-789_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-MSK-P-0018175-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:39:49.045696-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "10935163-56ad-43d1-af91-1846aa5922eb" ; + crdch:id "d4ba57ac-0820-4d57-85a6-06122bb4559e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -12499,22 +11530,25 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3f296a63-9ea9-4648-a621-c8fe8a6d631e" ; + crdch:id "6b3df15b-f5c6-4c79-923c-572688a90a50" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-cbxznf5u-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD1220_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:57:01.408534-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e0559edf-8fa9-43f1-acbb-7964ea0c33d3" ; + crdch:id "2bbdf4c4-88a1-4358-a88a-5daa2a9a506d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -12526,23 +11560,53 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6d9a9668-da18-4c45-a108-8b0b058ec47c" ; + crdch:id "45950ba0-9179-4304-9bf7-1a43880d000b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006284-4777_diagnosis" ] ; + crdch:value "GENIE-DFCI-010940-9514_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6b2d8256-f78a-4ac8-b0c3-a97a03410b59" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "8642c059-a648-4ced-977f-45d6e6496e7b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "0ea10d4e-1809-4763-b440-8e077ecab3e5" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD17629_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:55:27.721574-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "9ab974e3-bc94-4f83-b7dc-82285f5b4b69" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -12553,20 +11617,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5a157d1d-a316-4b42-8444-63e22ee704ec" ; + crdch:id "d4b595ef-5e2f-4722-bf4e-48bb831bc057" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-065d55ae-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-DFCI-002065-124_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7128ab9a-3a2d-4df6-8604-829406ab3bed" ; + crdch:id "172019a6-18cf-4532-89ec-9f4ec83dee30" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -12580,118 +11644,83 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f7be786a-80e5-5c78-af12-715c8cdd318f" ; + crdch:id "d4b70019-403e-5a16-b7aa-5ed71d54a517" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A718_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-6473_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ddeeb19e-1929-488d-8e19-c6212b3b78fb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "a9e7990e-7daa-4c79-a836-ac1ad63aaa37" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8f620b3e-2962-49da-bcaf-4ecfd9580923" ; + crdch:id "ed96ee9b-cf03-4eaa-b783-07b739e3a648" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "a88696d9-b36a-4fd7-b3ed-b6b31aa4094f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c1cb359f-50c5-527d-941f-328d1d34f062" ; + crdch:id "3ef5f7db-6234-5c11-96d5-fdb6cf8ad63e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-IQ-7630_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-5978_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3b35e7e6-0e30-48be-9d22-d95fb49f1227" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "b801368a-b10a-4a42-bda8-5df8216b532f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d81234fd-4e10-469a-81e6-f23a192f1ef1" ; + crdch:id "7560ec6d-e0f2-4b55-88bf-62e7173126a1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -12699,88 +11728,82 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bd97a61f-6744-455f-88cf-2a418f2458a0" ; + crdch:id "b33eba98-6a89-4454-9a53-94999cd5003c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "Stage IVB" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "stage ivb" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "N3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "Stage IVB" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5c73649d-f112-401e-a47c-785337555930" ; + crdch:id "230d872b-0206-409c-988e-6485dae90db9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-JHU-02535-03020_diagnosis" ] ; + crdch:value "GENIE-GRCC-p8qm5k95-sample-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T23:09:11.890404-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d34c6f0f-6b69-4820-8dc8-90d8d54ff7c4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "2d54eff7-a093-4bf0-b1c2-2f9f159e6b78" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Not Reported" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -12788,28 +11811,25 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Adenocarcinoma, NOS" ] ; - crdch:id "215314e4-f8c7-47e1-8993-f126c49bd1a8" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "a099ae58-fa38-4a90-82b6-c97a23b317f0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD7896_diagnosis" ] ; + crdch:value "GENIE-GRCC-f88a03a6-metastasis-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8140/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:49:07.730023-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d3811cf5-8f54-4344-9efc-2f42c49e4e67" ; + crdch:id "a9b18808-3ee9-4274-9a83-8d2fcbc16c7f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -12818,23 +11838,23 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9c1cd7ed-46f5-4809-a898-22cc0e15cd64" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "39076d27-3e66-4f32-a646-08d8e866bb8c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-438c3609-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-GRCC-5201a20a-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8010/3" ] ; crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bc168208-ee4f-4a50-8ddf-b72b0dd59da2" ; + crdch:id "68c9aea7-2d45-4200-b2e5-02aa0ab64d09" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -12845,171 +11865,251 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "4679b4bd-c891-5a60-9b12-1e6bf1bb7675" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "c97d4793-3b4b-521d-a274-2d1dfeda79ae" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A4IF_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-7398_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5eea7c58-96b4-426b-9685-15599e534730" ; + crdch:id "13348e4e-8b8e-44b5-83e6-a1159a53ea35" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7bfdae74-2bf4-4ec7-b08c-acd9b9e0baf4" ; + crdch:id "251e8544-2c3c-4b31-a2b4-29b57e6ee4fd" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c8cffdf6-7c37-5146-9bff-2cbd5a6f5bbd" ; + crdch:id "af8fdb73-f4a3-5b32-b9d5-6f9d39a97856" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7364_diagnosis" ] ; + crdch:value "TCGA-D6-6824_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a17406af-2eda-4148-8a0d-ec2ae4bd9fac" ; + crdch:id "10c45c93-36f6-4085-8bc8-f46dfdedca1f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6ced7677-159f-4e9f-b550-627ab9ea80f7" ; + crdch:id "4d8bbfbd-1a39-4630-a1e5-3bc6abb01949" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "2e1366b9-95b7-4a0d-81f0-7ec14e4f4592" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T4a" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "09ac3334-b77e-56e2-a46b-57faf703f1fb" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CR-7385_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d1553b1a-bc1e-4dcf-a273-b3effabe380b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "4c4a6867-babe-4032-a639-a9b31cdddc6c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "NX" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "98a4badd-be86-5ac9-b0d9-9099d5bdcdef" ; + crdch:id "6bbf8ace-0b17-57e5-bf9e-2c164cb28e53" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7247_diagnosis" ] ; + crdch:value "TCGA-F7-A50I_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -13019,36 +12119,41 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5ec51826-98c1-49d2-a990-7a95ee636753" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2e9cdad5-53ec-4b5e-8a1e-4f8abee04149" ; + crdch:id "ccd8f2ed-5a6a-460f-b692-ee7d78e29b18" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f84ae44b-4bb7-4841-aee0-139cd79b9680" ; + crdch:id "384902a7-fa03-4083-9baf-7ce114694c9d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "13da732f-058d-4635-a2f0-81e73c725b8d" ; + crdch:id "5eb175ff-1b47-463a-8f16-4b59914457bc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; @@ -13057,66 +12162,36 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "11781aec-74e7-44bc-86ce-9941aa62b6f7" ; + crdch:id "a1439fe2-31b2-4a31-973f-fbeeb13a965f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-1594-3307_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0001405-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:00:11.934564-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4cb8fa37-e3cd-4d7e-bb34-67ffdf228d78" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "5dcad3f6-29d1-4043-8bf8-c8ceb17c5ec4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -13127,172 +12202,94 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b725e6d2-92c0-5585-9de7-14bb623b472e" ; + crdch:id "9e30aa6c-91e6-5dd3-9512-75c162a89913" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4738_diagnosis" ] ; + crdch:value "TCGA-QK-A8Z8_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8277e744-0508-47d5-9cea-11dcf7f56d35" ; + crdch:id "cff6967e-e8f7-4a25-aa31-9328e4b42816" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "51622170-a903-43cb-bc38-4d40c7ea170f" ; + crdch:id "1efb2d28-ac51-4d70-a24d-667a2b53467a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fb06ae75-8516-4cdc-ba9e-093444907fc7" ; + crdch:id "a118da56-784d-4b67-aade-d9a7a8b49f18" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; + crdch:system "GDC" ] ; + crdch:text "M1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage IVC" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "stage ivc" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "M1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f543ba05-0134-4222-bc49-da336358e2e0" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0005862-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "fbb548d6-a035-43c3-99a4-7fb2892ade49" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "664c73af-7fd8-43bf-9a1c-1109c71a303a" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-6a5b9e32-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T18:19:50.810302-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e6616639-64a7-4462-9676-1b2420f371d6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b8f93296-f293-4af4-83bd-6ae35aebe59c" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010368-9817_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "094236a4-db5d-4e05-b020-5136ee6f4225" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Stage IVC" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; @@ -13340,12 +12337,6 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -13357,25 +12348,31 @@ crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ] ] . + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3d039654-a9ad-4641-b459-bd7ccd1ec1b6" ; + crdch:id "99aa5d5b-c650-47f5-b485-da3d78661529" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-NKI-MCU4-LAZM_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0018925-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-29T19:51:14.064673-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:42:00.849990-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b34b2488-73cb-480c-a1ac-c2ef5b89c5f0" ; + crdch:id "5007e321-c75c-45c2-b4a7-0d3cbde5280a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -13386,29 +12383,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "1fdf9d03-4341-4aaa-b47a-98f1221816ea" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "64bd8ea3-d4cf-4e2c-9d2e-77dcadd5364b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD3249_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-008227-5962_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:00:26.233095-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "425f42d0-0349-42bb-9072-cfb0bd97e922" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "2386e3a8-c4ea-4434-af11-e60fae9630fc" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -13416,26 +12410,29 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "8932404c-6adc-4b1d-81fb-fdb4dbb32ddd" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "d2578ad3-da53-4f9a-a3b7-043e9c01a282" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008185-T01-IM5_diagnosis" ] ; + crdch:value "AD17065_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:54:42.853523-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3a9e0ea1-fb4f-47bd-bf6c-831f7101b005" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "c84c230b-7953-4d86-ba93-255ab2242ce7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -13446,9 +12443,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2c09a792-df0e-513e-a9a2-7e363de6435e" ; + crdch:id "1214a9ed-2d43-50a7-9a94-85eaa002670b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-F7-A623_diagnosis" ] ; + crdch:value "TCGA-BA-A6DA_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -13458,61 +12455,61 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "33c19ae3-107a-4b64-9906-5b775025cd8f" ; + crdch:id "a2260bc1-8aa1-442c-933e-e4a05d46d802" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bb90f8e2-c872-4ded-9d10-5110f023762f" ; + crdch:id "8b80b922-b00f-4cda-92a2-49c357aea89d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5f14a8c0-f19e-4a67-b6dc-907196ab34f6" ; + crdch:id "33bf2824-d873-442f-8ae6-48274fbf4a94" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], @@ -13522,33 +12519,39 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6c55b480-1444-4ae1-a079-72287e8794a4" ; + crdch:id "52fd0265-204c-4ce3-bb51-a3cbee5aca51" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0017687-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-GRCC-115ef99e-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:37:32.909734-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "52f200af-cd9b-4d63-91fc-7bf44c67c537" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "6ba7ff9a-775d-4239-884f-4a303b42e4fd" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -13559,20 +12562,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "32bc08a5-7441-4dfc-b13c-9e193e5a7ac9" ; + crdch:id "4e9b9fad-2d73-4867-b7f8-8e42769ea41e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001682-T01-IM3_diagnosis" ] ; + crdch:value "GENIE-DFCI-009088-5942_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b2a64027-92cc-4961-9c27-821fff58c5ca" ; + crdch:id "cc6054a8-ec09-42af-be24-4041b7be75cc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -13586,229 +12589,134 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "a2cd4aae-5655-4082-956c-f5bbc733c576" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-UHN-221761-ARC1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5103a1f3-d342-462e-9845-9703579d26f8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "39076d27-3e66-4f32-a646-08d8e866bb8c" ; + crdch:id "6fdb9066-4bcf-42aa-81d1-585b2f2fdaf9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-5201a20a-sample-a_diagnosis" ] ; + crdch:value "GENIE-MDA-6209-17288_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "68c9aea7-2d45-4200-b2e5-02aa0ab64d09" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "514322a5-47cf-5d99-8ae8-f4466bbad28e" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A6IF_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; - crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "bfbfb315-632c-43e7-ae3b-61bcd82b0d3b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b3a8b960-6807-42ec-b6a8-492d58de2b86" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5e77db09-dc35-4cfa-ac78-0f7af0b742ec" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Not Reported" ] ; + crdch:id "0f97f0c0-2148-4c06-97a5-37a64ed1b81d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "6739697d-d536-5d38-813f-5a4973a97cb9" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "72d80059-302c-57fe-89fa-10045543f0ad" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A49A_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; + crdch:value "TCGA-CN-A6V1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Palate" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8e00c51b-cc4e-4de3-ad9d-8ffe30f2ab0b" ; + crdch:id "8f952c62-2404-484c-b8af-33ce60f4e024" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "77234a56-cad6-4b84-aabb-032be68f7dea" ; + crdch:id "b2ad9679-048c-43c4-9d78-45638ad5a493" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4b" ; - crdch:system "GDC" ] ; - crdch:text "T4b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "64bd8ea3-d4cf-4e2c-9d2e-77dcadd5364b" ; + crdch:id "11f5b868-a6eb-4575-b5d4-54cd8a406293" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008227-5962_diagnosis" ] ; + crdch:value "GENIE-DFCI-027923-87624_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2386e3a8-c4ea-4434-af11-e60fae9630fc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "4e763f63-0494-4b2f-9f6a-c9461c7e7b1e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -13819,101 +12727,47 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5202e65a-e9af-58ee-8960-9190089fb197" ; + crdch:id "57e78d94-5a02-499e-953f-e5539884009b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6467_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-036456-74857_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5ef4d047-5a84-4e03-acf5-02029d8a4cf2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-27T19:26:40.896040-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2d9ad43c-f177-455e-9b63-1b9ffdc672d9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "6f3b4fcf-0519-439f-b3e9-6a0678745885" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d7acd35e-0ca1-42f0-932c-a3cdd6f8d09b" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "4228d736-f7fe-4ef9-8bce-39b8c6c3bc70" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037833-36073_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0010459-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8f775235-6026-40f6-b156-cc3711222412" ; + crdch:id "d69183b2-2961-45f3-a4db-3d32d08f6abb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -13927,115 +12781,118 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "da5ce97d-de12-5384-a88d-a9874b39b7dc" ; + crdch:id "45ebf5cb-a072-582b-8ace-7cd198806bc2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A64Z_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; + crdch:value "TCGA-F7-7848_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Palate" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "eb25346e-0e28-4161-94c8-916b41f8d969" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b99fa26a-da90-4b98-bea0-f0c71a1b6ea3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "95525590-0eea-4017-be66-dc487b78299c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "8aa78dee-bc22-4d4b-86d6-60fb80358da8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "67289d96-8140-4ba1-9863-124950488c1d" ; + crdch:id "f7831fa0-1f1d-4623-aba0-8117b925a1ee" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ] ] . + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cb7a6350-80e2-4b6e-9b86-05632255db52" ; + crdch:id "c1887ffe-1e7a-4584-a9cb-897604949138" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003213-4767_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD7475_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:48:10.807261-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a764b89e-ad60-4316-a812-24a5eec7b9dd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b82784b8-217d-487f-b2f6-4435ebc09885" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -14046,20 +12903,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "58498007-02e8-41fb-b884-2383b5eb1414" ; + crdch:id "f9e5f978-310f-4011-86bd-f468da998bd3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007582-3990_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0015030-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:44:49.261364-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:42:39.927651-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f198873e-fb8b-4ddb-8d79-1fcf1bb1d764" ; + crdch:id "e3362d03-8d6c-4be0-b1a6-5ce9c230f4f0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -14073,130 +12930,74 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4176108f-948d-5715-afbb-cc21f3cbfaf5" ; + crdch:id "4ac21d4b-c592-4afd-bfc1-278702612bd6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5363_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-004838-2080_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "591e99ec-46f9-442d-ac20-745dccc8a52b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d0161f8c-9c53-47ad-895c-40d1be3a814e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "5e4e1e21-8016-4e27-8f72-2411714203e8" ; + crdch:id "10d245b5-b16d-40ee-bd41-bd08a0355894" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; - crdch:system "GDC" ] ; - crdch:text "N3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; - crdch:system "GDC" ] ; - crdch:text "N3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3896106f-2770-565a-b872-0d61198bb107" ; + crdch:id "7a67eecc-6f46-5181-8b64-c022d0fd0060" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5442_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; + crdch:value "TCGA-BB-A5HY_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Palate" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "698208bb-7272-4ad5-9cc0-909cb669bdaf" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "589cdde1-ecd5-4a7b-9cbc-3186916822ab" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "26243d14-e401-4ca4-92e7-aee13c9e6e47" ; + crdch:id "5c2b4403-cdd4-4550-ba01-d8ebad9fcbc8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ec885af4-3513-4790-ab1f-6ecc94b6115d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "4467ee1a-7188-49d6-a0d1-c8e395e6cabb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; @@ -14214,54 +13015,111 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "d68e9ec8-d562-49e0-abf1-ebc41a0f439a" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-006509-3496_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3e441a98-f869-414d-9732-4b4037711d5e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "545abbb1-03c0-4b81-af21-3ebb7a5bb299" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD4812_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:53.493092-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "4288c5a9-610c-4b1f-b102-2b96b49a6fd8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "36009b16-600e-42f9-9509-783c76c5b88d" ; + crdch:id "49cde226-3d69-415f-ad98-02d190dbf75c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-034499-159099_diagnosis" ] ; + crdch:value "GENIE-DFCI-006446-3455_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bce047a2-b5b7-4ccf-8bf9-406d8c87d7a3" ; + crdch:id "5c19b5fa-d6eb-4d7e-b617-930e19aea484" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -14275,53 +13133,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4ac21d4b-c592-4afd-bfc1-278702612bd6" ; + crdch:id "48e8dd81-ed4d-5c54-af66-84e86477d5c8" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004838-2080_diagnosis" ] ; + crdch:value "TCGA-BA-A6DL_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "10d245b5-b16d-40ee-bd41-bd08a0355894" ; + crdch:id "dc102dcf-3f48-49e2-8a6f-cfdc34f8ed0f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "bd90f967-84dd-48cd-aec0-9de9a76df7a9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "256469d0-5f36-4966-bf4f-3b4297e55f43" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T0" ; + crdch:system "GDC" ] ; + crdch:text "T0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "eb8958ba-0798-5ab3-b4f4-258d441d7e03" ; + crdch:id "c127a1e6-f25a-525b-949d-013bac98b38a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A6T5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "TCGA-DQ-5629_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e45c81dc-4143-4e97-8212-85032c760221" ; + crdch:id "57ea3eed-f8e2-4310-90c0-50d89f818a12" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c98f1b7e-5d3c-4e07-9d9c-65c5a6ac6cd6" ; + crdch:id "769f3c1c-323e-4f04-9ae7-e41f484a964c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -14329,40 +13246,40 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7fddfc05-49ef-4ebc-8572-05059a5fc363" ; + crdch:id "cb2da33c-021a-4af5-8509-118bc1e8e0d5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; - crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; @@ -14374,184 +13291,189 @@ crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d0678ad6-4a4a-4ec8-9e5f-352c1347efc2" ; + crdch:id "b1c3bd39-9f13-5dba-aeeb-86271bf64b8d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-a8pxs0u6-sample-a_diagnosis" ] ; + crdch:value "TCGA-CV-7242_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T18:19:50.810302-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a45efd70-9bee-4c18-82b1-666d2c1eb781" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ab9d819a-6445-4bad-a520-3d1edf413508" ; + crdch:id "6b4b146e-e6c5-454d-9c4f-66a6f851c3fe" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "59b73fbd-93ab-5cbb-b052-82d5e66a4c16" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-5249_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6697dd71-5a58-4862-b26e-ea16dcc383f2" ; + crdch:id "4fdddf85-30de-4666-89d2-0683e9264d6d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b72390d2-f19e-493d-9a30-cd81dd232188" ; + crdch:id "f9dea7a5-e9d2-48a6-bbc1-c5c1f8e7ee67" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "Stage II" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f09803e3-8795-5077-84ae-bf0666bedc35" ; + crdch:id "5d448af8-7478-4252-9043-772077929480" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5435_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-023766-23966_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d2491655-a4a1-4e4b-8f94-f50dc1c5d64c" ; + crdch:id "a3ca3ea8-6ea0-4585-8a50-294ca4c87a24" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "d9cc35a1-8103-5f6b-8d97-cc64c564c677" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-UF-A7JH_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cbcd3026-9f65-45c1-8fd8-d08f1b6b065e" ; + crdch:id "980726e2-9e0c-4212-b5aa-69e139fc3be7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "78a9bb84-9d21-40d2-9b0b-1ba8d888912d" ; + crdch:id "2b803b39-f13c-4335-9845-05bb61830015" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "14098d2a-e40e-4f1a-bd76-f8bf7c339ee5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "1c9d867a-6fba-49a1-99ba-63bd01942397" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; @@ -14564,21 +13486,15 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], @@ -14592,106 +13508,165 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a66ce9f9-d7d0-5f2e-b0c0-73f306f68236" ; + crdch:id "5a157d1d-a316-4b42-8444-63e22ee704ec" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-6869_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-GRCC-065d55ae-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-23T13:20:20.149518-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2f9729e6-edea-4612-82b3-01251317074a" ; + crdch:id "7128ab9a-3a2d-4df6-8604-829406ab3bed" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] a crdch:dict . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6ca9116f-412c-41d9-872b-1775f3d9464c" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD11803_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:01:51.025011-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f4ed2c84-39f8-4ab3-8762-a9920acc2432" ; + crdch:id "3dac18fb-752c-42aa-bdad-9f91d54fb950" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6788d692-193d-5d61-975f-1a79e54439ff" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-D6-6516_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:system "GDC" ] ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "2d8d11be-421d-4f96-b5d6-4cbc632f11f3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0aaa8bba-f4a5-4158-b9b4-a02244b5f6f7" ; + crdch:id "c129394b-3c04-4a6a-b4ea-d56d96bf28ef" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "c3c82c51-0200-44c8-b5aa-050084983398" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "stage i" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6fdc7de3-3d2e-459a-94ea-1dba9572f47d" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "43aa2ba4-d59e-4e9f-9b1f-009fba8ee08a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-480293-unk-1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MDA-4754-15863_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "116b69cf-c9f3-45c6-be86-c4f22a36dcf8" ; + crdch:id "c3431e69-82eb-4eef-9e13-312bfde95103" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -14705,20 +13680,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "64017f79-8293-4fd3-8af0-bf01eb6cf49c" ; + crdch:id "605addeb-a295-4bd2-ab90-347c41e9b1ad" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-UHN-653571-ARC1_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0008105-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:21:56.842750-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5349f1ac-ad8d-437f-a9e7-30b2323bd11f" ; + crdch:id "b9b1b672-a788-46eb-bc8e-a5b401d1a430" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -14732,164 +13707,124 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "155ca101-ad45-4f50-b9ac-45908daffab8" ; + crdch:id "1f6860df-38fb-5519-8ec9-3068b0476cf2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003009-T01-IM3_diagnosis" ] ; + crdch:value "TCGA-CN-4735_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f8de95dc-1011-4b86-9a46-28bc46465195" ; + crdch:id "fbb300fa-8793-42da-a68e-4570ae2e5186" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "21b7042c-de33-572f-a77e-98db817efd44" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6492_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; - crdch:system "GDC" ] ; - crdch:text "Palate" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2da6f33b-4a9f-4cf6-ad8f-873be656a6f8" ; + crdch:id "a2caeab5-55a4-412f-a647-0112f48bbbe7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9d258494-fb84-4435-aa3a-f5778ac061c5" ; + crdch:id "feb21d9d-394f-402d-8659-eb15bb95f0db" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "M0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "6284d2ec-e8b6-5cce-957d-f55704379de9" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "91287016-0fd4-5434-a010-e392bd679282" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-TN-A7HJ_diagnosis" ] ; + crdch:value "TCGA-CV-A45Y_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "50df1144-990e-4357-8a15-132289bce0d8" ; + crdch:id "01a4aa4a-f073-435c-a411-839760cbcb9f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cdc66ca4-8864-4f22-bc4e-8fb5e073937f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "26026e2f-b112-4535-97ac-6956cb267e9e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "412fe306-9755-4efe-abb0-9af695b5691e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "bbcc5141-d805-457d-bc4a-d424c8c39cb7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; @@ -14898,228 +13833,364 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T4a" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f8933756-4001-4c7b-94c7-2d8964ffda9e" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-005118-1198_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "430338db-7df9-43c8-be80-6ef5a6b98899" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4b90baa1-cf87-5186-9101-0464aec143d3" ; + crdch:id "35adcfa2-f4ae-4aec-8362-097fab231545" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A4IG_diagnosis" ] ; + crdch:value "GENIE-DFCI-000205-461_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ab00664b-8f6a-493d-b000-89f1341dc713" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "c0dca6b0-81eb-598e-9514-f23513df1ab8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-UF-A71D_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c029272a-feef-4a11-9566-092c16b40eef" ; + crdch:id "e4157201-93f3-4f08-b3a9-dacb22671a57" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ce469c00-b5c0-4d7c-875b-092c5b6ac289" ; + crdch:id "297ea792-1a29-44db-a14b-38513b50826f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "87d8fec9-7ac3-4359-a6be-de270584ac1b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "87e9b232-8b59-573b-9758-c7b5456d6fc0" ; + crdch:id "881c2131-1f0d-4b11-8b3a-626918ad5566" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7248_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0013652-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "791203c3-4192-4844-b32a-0f21944333e1" ; + crdch:id "4c4f2c9b-d2db-42ab-898d-7d6c8c8e4a6e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6307ff41-9bb5-438d-8789-a73b41303d64" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-036509-75021_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-27T19:26:40.896040-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "24a2dd45-0453-4bfa-af4c-cde8cb0c0cfb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "ba40b824-5fe9-4a73-b7f0-9b371af64f65" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "514322a5-47cf-5d99-8ae8-f4466bbad28e" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-QK-A6IF_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:system "GDC" ] ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e5ab53bf-073a-49e7-9402-8e7261d385c8" ; + crdch:id "b3a8b960-6807-42ec-b6a8-492d58de2b86" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "bfbfb315-632c-43e7-ae3b-61bcd82b0d3b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5fe254fc-76cd-4081-a46f-574f2ec76d10" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "5e77db09-dc35-4cfa-ac78-0f7af0b742ec" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "b4c405c4-ece9-4cd9-b11c-cb1f863021cb" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-003788-772_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f933f399-d986-43eb-bdc0-b3faf49bf513" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "59474381-516a-4be2-8b74-7fe5804ec371" ; + crdch:id "a84b9519-37b2-4311-ac32-8151ae7261e7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003795-3691_diagnosis" ] ; + crdch:value "GENIE-DFCI-090167-282584_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:52:12.528526-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8212fb32-9c81-4bf1-ab6b-337196acdf90" ; + crdch:id "0f1ec484-9205-42f4-9696-815dae75b073" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -15130,29 +14201,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "b0113a66-8202-482a-ad65-dc55cdca3c27" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "09912a9d-8fe7-4170-89cb-f0881ba681bb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD8711_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-037012-88553_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:47.854910-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3ece7ea7-cad2-4e6d-811f-c91f63a4fca9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "89c7b64b-262a-440c-b2b0-b45a94097d6b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15163,20 +14231,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "605addeb-a295-4bd2-ab90-347c41e9b1ad" ; + crdch:id "664c73af-7fd8-43bf-9a1c-1109c71a303a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008105-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-6a5b9e32-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T18:19:50.810302-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b9b1b672-a788-46eb-bc8e-a5b401d1a430" ; + crdch:id "e6616639-64a7-4462-9676-1b2420f371d6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -15190,47 +14258,106 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "03f214c1-e688-473f-b84b-5864f56a6a3a" ; + crdch:id "c7db86f3-b6c1-59db-961c-534b91393b19" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-001000-1570_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-6010_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "cece12a4-5f68-4a6d-8815-e88495da08f4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "cd2a5d45-9bae-4c96-b8dd-7ad079153a49" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "016681b7-82cb-404f-a175-8cb6d3f6bc62" ; + crdch:id "904e12f8-ab59-4ad8-8096-7b82f9388d70" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fc929f30-0322-43c4-b12f-ddff9d8a2335" ; + crdch:id "8bc744c9-1120-41c6-a782-3bda1bbfa2ce" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010590-8636_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0012578-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:17:29.664139-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "175e9244-58cb-4b1a-9614-a4fb1c0e6603" ; + crdch:id "31be6816-e615-4939-8c64-c523db6a438e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -15241,26 +14368,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "83347eee-7d6a-4848-a139-a71f053e92c9" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "82cf8f30-edc0-444a-9607-498f1f4fc6a5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000768-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-NKI-ETWO-SK3U_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fd2acd96-a021-4fd4-b0f5-1d9f6e4448bb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "92e24628-56bc-4c65-9c4b-76c589943948" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Not Reported" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15271,26 +14398,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "601e60c5-25a1-41e7-a47e-2a069cb8e099" ; + crdch:id "27b201c5-0310-4f7a-835c-31fde311cde6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD11228_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0020040-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:56:48.362532-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-02T20:58:03.565619-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b62623cd-3d81-4e48-bba4-7df880930106" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "8738d7cc-e80c-4a00-bc4e-fee451f4b19f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15301,44 +14425,70 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d4b70019-403e-5a16-b7aa-5ed71d54a517" ; + crdch:id "2457e378-c4bb-516f-8966-82e1453eafd7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6473_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-CV-A460_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ed96ee9b-cf03-4eaa-b783-07b739e3a648" ; + crdch:id "b1c47b2e-ba48-4f1f-b07e-f930b1135201" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "904d5793-ae7f-492b-aaed-ea6cca865d63" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a9e7990e-7daa-4c79-a836-ac1ad63aaa37" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "9e397756-8535-40f2-9fc8-d0f1392a5e6d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], @@ -15348,98 +14498,87 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "M0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c9ea5a2b-8b14-5745-b9c3-c93c9abe468f" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "d0d35a5e-572f-4cae-a0df-67ce30803048" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A45O_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "AD14308_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:41:59.431029-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "77b774a4-9456-4907-86e6-9ff2dd87b8fd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "ec7fe5e6-74af-4bd2-9ecb-8e302f763b22" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "fce64b88-8be6-4710-83be-18c9afdf13ed" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "32112d7c-2b29-485d-86c3-6b995450ec8c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "38c088b1-bab2-4d5c-8f45-80280d1c309b" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-010800-9387_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b480938b-4562-4d37-a280-16cd4dc700ca" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5b518f0a-dbef-4346-b463-b59bd735a311" ; + crdch:id "9233f502-9580-4801-915e-732ca0f26a2c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009367-8081_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-050720-203425_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:18:25.269226-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7230cf9f-1930-4377-bfdb-6e07cd472bc0" ; + crdch:id "c1353660-3a6c-4a01-8800-d52a40b6ed68" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -15453,26 +14592,33 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7ed3e77f-cc81-56cb-b573-cc6df309ff48" ; + crdch:id "f09803e3-8795-5077-84ae-bf0666bedc35" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-4227_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-CV-5435_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a6748675-5433-4f39-a578-9a1ddb8bb1b3" ; + crdch:id "14098d2a-e40e-4f1a-bd76-f8bf7c339ee5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d2491655-a4a1-4e4b-8f94-f50dc1c5d64c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f31d010d-cb3e-46da-9647-38fdb9d1bbc0" ; + crdch:id "78a9bb84-9d21-40d2-9b0b-1ba8d888912d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -15480,82 +14626,82 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0e81b0ef-6f16-4a56-9f18-8acad8bf9ccf" ; + crdch:id "cbcd3026-9f65-45c1-8fd8-d08f1b6b065e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ca8d9936-f4d9-465a-8640-66a91f735a60" ; + crdch:id "a0943f40-a682-4318-bc07-eea80150867b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0018419-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-DFCI-037288-116439_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:39:49.045696-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:26:11.717995-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "60efb1a2-a8b1-40a7-b230-e4b532a8048b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "8449ccd3-033e-4c9f-bec5-9f341264e12b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15563,26 +14709,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "494e7724-f0c8-44b8-a4f9-8e6cc9a2c095" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "155a3146-d68b-4058-abe2-3ae8713641ce" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-NKI-FGHG-R6TZ_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MDA-5361-16435_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e91ef1f0-a986-44d2-8880-fbef0afe91d8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "a7b07575-200a-4a32-8faa-075ded8667cc" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15590,23 +14736,23 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "f2f2d6b1-7233-433d-b34f-62a8d4e50b0c" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "5b518f0a-dbef-4346-b463-b59bd735a311" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015645-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-009367-8081_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8a8010f9-2193-4604-9425-da6e5512ebef" ; + crdch:id "7230cf9f-1930-4377-bfdb-6e07cd472bc0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -15620,26 +14766,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "acb41bec-39c8-477f-8cc2-b8c982bf5b2a" ; + crdch:id "3439abcc-0169-490c-8794-73e53b937d7c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD9755_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-037577-74790_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:57:54.983619-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2b14983f-b848-45de-9881-5dc4f483f7a4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "4121fe4a-1ae9-41e4-954d-88c88d047d9c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15650,171 +14793,116 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "28979d39-3da1-556a-9b82-2a9953b57989" ; + crdch:id "c8b3a37f-01ec-481e-9460-0bcac22cc002" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A5QF_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "GENIE-GRCC-18076aef-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "903ed81a-057c-41ad-93de-aaa9d9c082c5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d30d7d4c-0acf-4b61-9d7e-2c15e20d73a8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2e51af26-4d06-4b66-be71-0bebed2e4557" ; + crdch:id "960fe012-e237-42c8-a3e0-d02853ce3818" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; - crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; - crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9461c5ae-cbec-5810-b0a6-9644168accb4" ; + crdch:id "31489596-1797-567e-814f-ec85278ee342" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4723_diagnosis" ] ; + crdch:value "TCGA-CV-5432_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "c552cf29-896d-4a47-8022-e5c57e27e70e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4a485f87-1a73-42ec-af0d-0b6de2b23504" ; + crdch:id "418aadda-9f2f-43be-b171-866585aab114" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f4a14404-3545-44fc-953d-e441139e7fda" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3a13692e-cb77-464a-8ace-cba47f99247f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4db1536b-23d0-48fb-91f8-248a03f58aa4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "b4a36114-80d3-4f28-b85a-077dc31eb485" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "stage iii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; @@ -15822,26 +14910,26 @@ crdch:system "GDC" ] ; crdch:text "N0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "d50387b2-938c-480c-8287-6c8754e06278" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "a69046f9-49c2-4846-a394-ffebf61b0340" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-6686-17868_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-001847-1155_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2022f8c2-108a-4919-bbcf-1dd1ba4fa10b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "ae00c91b-f03b-41fa-bd2f-d6fde4338cf1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15849,56 +14937,53 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Malignant rhabdoid tumor" ] ; - crdch:id "d1368e23-4a00-5b0c-ad28-56a5a4dbd833" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f068b7ad-5b43-44f0-95b3-33ead995b8cb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TARGET-52-PATYUA_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "GENIE-MSK-P-0010161-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8963/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "83a37c0f-ac29-558c-b7dc-a9fcfed82b61" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:id "ea42167d-71c9-4eda-8153-2b207208d97d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "unknown" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6579daca-0ec7-49e8-92e5-6a6b7c379b8d" ; + crdch:id "49934fcd-822a-4e1f-ab12-46ef9216779d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-h39utsgs-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0009754-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T18:19:50.810302-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1f1c82de-2931-4f38-9caf-213d5425ded1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "7c2babfc-9948-4332-8c28-096971073c2e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -15909,101 +14994,95 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "843f33f9-e390-52bc-90c8-fba0a4557916" ; + crdch:id "3bd2d2d4-7d4a-51f3-bfaf-4153b96110ae" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A7JV_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-CV-5443_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a1d62ba6-696c-4693-9067-d4226a4e6316" ; + crdch:id "f70fece0-2fb1-4d8f-955b-7b9bbfeb9755" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c312a7a4-ba29-49a9-b4dc-876505a6a6c4" ; + crdch:id "746322c7-fe75-4b9f-9309-93e9cfa4cb5a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "eed0dcf3-36a2-4890-bb02-e8b56ba4d8d8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "4863312a-043e-418e-812d-2ae2a1f66f29" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Solid Tissue Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "stage iii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7c7482aa-6349-58c9-ab17-6c69acbd579e" ; + crdch:id "26ffab97-fa9a-5135-b283-8c4aebe51a26" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7388_diagnosis" ] ; + crdch:value "TCGA-CV-7250_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -16013,77 +15092,101 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f27e3255-bc73-4943-8201-5245b85c4ee5" ; + crdch:id "6f55766a-d980-414a-be4a-369e93ec3436" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3e6bc216-301a-4f24-911c-8c3610e4a015" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c6aafc51-6295-494f-9bf2-1e4f43a72ae0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Not Reported" ] ; + crdch:id "f5472b70-32c8-48b0-9051-f9b33272ffd6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b4f8ddc9-0ab4-447e-8292-5dcf8a9085ee" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ] ] . + crdch:text "Stage III" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "b03c5a4b-9dd8-4186-b8d5-a65acb317474" ; + crdch:text "Adenocarcinoma, NOS" ] ; + crdch:id "78daf8d2-f74b-4d9e-9ffe-79e90425ad3c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD3459_diagnosis" ] ; + crdch:value "AD7638_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:04:01.286185-05:00"^^ ] ] ; + crdch:text "8140/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:47:53.195932-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c54fca3a-3919-4ac7-81b6-f1cf955f47a7" ; + crdch:id "a4ae0499-714f-4d0b-95b5-e085bb652117" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -16100,213 +15203,98 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "25fb47b9-2f00-4140-92bc-462b1e8447c4" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-4wf609jo-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0ef8dcd6-8f67-4f29-a69d-d952df3d43b3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2e4427b7-e557-49c7-85ef-39a02c4a441c" ; + crdch:id "b725e6d2-92c0-5585-9de7-14bb623b472e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-050738-234120_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-4738_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:18:25.269226-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c6e1507a-83f3-4c51-8275-319d0dcd8f97" ; + crdch:id "fb06ae75-8516-4cdc-ba9e-093444907fc7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ea9b7e18-cbc5-4588-8b59-d32af85db2c0" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-052774-173461_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:20:30.865187-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f37609a0-84b8-4203-9497-9f60cc8be539" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cf19d9da-2868-599e-9281-91b9e064078d" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7374_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ece42fcc-b771-42af-92c4-39fd74b645c5" ; + crdch:id "51622170-a903-43cb-bc38-4d40c7ea170f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "77be0d91-0525-439f-bb34-3a0702c81085" ; + crdch:id "8277e744-0508-47d5-9cea-11dcf7f56d35" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; + crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4a315682-7cd0-4c42-9fd0-50ec841a059f" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004723-1663_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "1291884d-38d8-49cf-b16e-aeab69d83681" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "230d872b-0206-409c-988e-6485dae90db9" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-p8qm5k95-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2d54eff7-a093-4bf0-b1c2-2f9f159e6b78" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b27a395e-c9b4-5903-afcf-90ba31fcdeb2" ; + crdch:id "4b90baa1-cf87-5186-9101-0464aec143d3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-HD-7753_diagnosis" ] ; + crdch:value "TCGA-BA-A4IG_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; @@ -16316,97 +15304,89 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e723f1bb-73a3-4d65-bd25-de76138515e9" ; + crdch:id "ce469c00-b5c0-4d7c-875b-092c5b6ac289" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7fb56f25-873d-475c-9db6-f0be3945d926" ; + crdch:id "c029272a-feef-4a11-9566-092c16b40eef" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-25T15:20:17.640379-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "698f639f-c34a-4f21-8306-26002008804f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "N2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "842d6984-7c03-4ab6-95db-42fa2ea699db" ; + crdch:id "770f08b4-6ea7-4cb0-a423-75909447e60c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010671-11105_diagnosis" ] ; + crdch:value "GENIE-VICC-518360-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T13:56:37.232985-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6f9eeaa3-8bd1-479c-a0fc-98317eb458dc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "75fdf08c-00e0-42dd-a21c-62cceb7bf00f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -16414,130 +15394,142 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "faf259c7-d577-5ef8-9075-9a42f1083260" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "afec3d92-5a3c-5b04-a2f1-49031942cc1d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-F7-A622_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-QK-A6IH_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Gum" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "32d7cb3d-5f5a-474a-9dcc-3b5f2dc64d22" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "63b4690f-f247-4874-9923-e96375c56a01" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3901d8b6-f2f2-45e9-a40f-3ccd679f701e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "0d0194eb-d83f-4028-9b4b-3308c0207133" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "32056265-c5fb-4544-9f99-22b34febb805" ; + crdch:id "5f210369-1839-4f18-b081-974efc7de032" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4b" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T4b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ] ] . + crdch:text "stage ivb" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, spindle cell" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, spindle cell" ] ; - crdch:id "d80aa9c7-2a22-57da-87ef-750dd4c0b494" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "cf93d012-b0b8-57b3-8a55-7575dfde2b1d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-IQ-A61O_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-6989_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8074/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8074/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "24e39735-725e-4627-82b6-c56ff33e3465" ; + crdch:id "7ac8fb22-0a09-4b16-af8c-b5c2e90a968a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "eee85b30-6d16-4f53-aac1-b74f36a62d9a" ; + crdch:id "3570ac4b-b585-4262-b54b-137a2515c689" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "09e8433c-1f86-42c5-91c0-2512fc4a7fe9" ; + crdch:id "a5c6b30f-2aa3-48bd-8415-bdce2444e49d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; @@ -16546,33 +15538,27 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -16582,36 +15568,30 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "T3" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2707217b-5a4b-404b-97de-921526581d45" ; + crdch:id "4fdd25bc-4056-47f1-8eb9-7e572313ba5d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-2b4655c3-sample-a_diagnosis" ] ; + crdch:value "GENIE-DFCI-009927-9027_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "56e9e0e1-5435-4b6b-93a0-70564fe1aa27" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "c65b0cad-f2f5-40f2-a523-60374faf390a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -16622,20 +15602,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cee28001-9ebf-46a7-b387-e932076e5df8" ; + crdch:id "640dafcd-ca8f-4305-bd40-240ff476b75e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010817-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-006707-2784_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "08a27a81-561d-41f1-9d99-6266c1f230c9" ; + crdch:id "53e7103c-42c4-41cc-948c-b8e23271bee9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -16649,47 +15629,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "28fc2416-e276-4a4c-963f-1ff59d64fb44" ; + crdch:id "d234a346-038c-58a0-824d-22bfabb73218" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-a947c792-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-MT-A51W_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "91e56a17-b4e8-4ef7-b587-a83bcd8c062d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "03c6ac2c-c6b6-4041-a024-f2556fab62b8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cb69d223-6e16-4e94-8a35-b1197a261b19" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "d238e52b-b2e8-479e-b76c-a168136e0ef0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage i" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7bfa067f-69be-4a58-a8a7-98963ee8c589" ; + crdch:id "aa6e25a1-2d85-423b-a149-8cf11a6947f7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-493620-unk-1_diagnosis" ] ; + crdch:value "GENIE-DFCI-010697-8404_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "57a1d12e-9ead-43ed-8990-0fecb573d3cf" ; + crdch:id "22ef8279-1519-4099-ae13-ff430645c992" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -16703,23 +15748,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "415b0c86-82b5-46c1-b51b-00e701add732" ; + crdch:id "96e73819-3b05-4a68-90bb-ceb60d419d50" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008675-7728_diagnosis" ] ; + crdch:value "GENIE-DFCI-006296-6704_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b1a78f00-1eeb-4c1b-838f-fb8453112c5a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "51ca54fe-f436-4a88-a11d-ab0781666edf" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -16730,20 +15775,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9eeeccb6-c3a5-4008-a87c-006d2e1efa9f" ; + crdch:id "982f892f-104c-4948-8788-6c77775e53a7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008672-7091_diagnosis" ] ; + crdch:value "GENIE-DFCI-013165-23146_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6db9d94f-7868-4a64-b9b4-a5b95747c317" ; + crdch:id "27e33c39-2025-4573-9b0c-1bc774566bfa" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -16757,109 +15802,50 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "39fa27e5-b36f-50e5-b173-1bb73a1ba5ba" ; + crdch:id "2a826dce-5a83-46e6-8ff0-9c7597ff54d4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-6826_diagnosis" ] ; + crdch:value "GENIE-VICC-673077-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "1737989d-8463-4761-b111-53e4fd396375" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7aa13049-917a-4d7a-bceb-3c718ec8fb7a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:05:42.341898-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a31ecf7e-1838-412b-ac34-6fd8810739c9" ; + crdch:id "a5fa104a-bb1e-4e7d-a740-607fc803f4f3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cde79cd2-3aab-48ed-81a1-259a3cd21002" ; + crdch:id "e978fb2f-2b7c-4ac7-b4c0-fa527f8c4ffb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-122614-unk-1_diagnosis" ] ; + crdch:value "GENIE-DFCI-090186-282458_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:52:12.528526-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "71ba3119-c343-43f0-84db-4ba8787d316b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "1bee9751-cbcd-46d2-97ac-bbe9f4495f2c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -16870,64 +15856,65 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0501e7a7-232b-58be-9425-92f1ccd697a4" ; + crdch:id "fac833bd-36d8-5306-b322-92106575bfe1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4727_diagnosis" ] ; + crdch:value "TCGA-CV-5430_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5bae7161-8838-4b10-9210-02deaae4b9c1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a7257360-c4dd-4f59-bfb9-c8d593050146" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "4151c76f-9dcb-4451-a99b-889e0024f8b9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f102aef0-94b8-4d26-8055-35b76da9dd5f" ; + crdch:id "72f98dc0-3fcb-47a4-8c7a-52a7cd9d3fdf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cc2d6cfa-7640-44dd-a200-68fd9f9ee69c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "5d293d68-61ae-49ad-bfcc-e0bdb91cc29e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "N2a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; @@ -16940,12 +15927,18 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -16956,109 +15949,250 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "706b1290-3a85-54ea-a123-e8bd14b085bc" ; + crdch:id "24e37f06-2587-52ee-bcb3-40688978538e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6012_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-BB-A6UM_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "badeaed0-2625-4a4d-bb95-d295e2c32c01" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "c4aabbde-a46a-403e-b974-7b61b964a1b8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e23c7006-1a13-4211-8920-47548641e574" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "ccc0e6ba-cf8b-45e4-9f0b-dd2422b3e470" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8b2588c8-4261-492b-b173-2490a5de668f" ; + crdch:id "99404948-9837-40eb-bf38-c1cfe1b9a88c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; + crdch:system "GDC" ] ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "stage iii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage III" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "ce63ab25-f6d3-475c-abca-986d8d91b869" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0019055-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:42:00.849990-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b5793531-8ec1-4bd9-9544-57844ebee0a6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "e071dcbc-10af-49bd-86cb-b1c8ec549487" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0017414-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:20:07.713564-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ff1a3e50-533b-4228-a8fb-93af76ca4b59" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "d7d13cee-ba1b-4e36-a0a5-3f925c871020" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0013833-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b6ddcf15-8ecb-47ca-bb29-60b9b43fa7aa" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "80c00d5c-1297-43e4-bbcc-cc895915ec2a" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-51823bc5-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "8d24d0d3-ec37-4b8e-9c31-e23965637da9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "cee28001-9ebf-46a7-b387-e932076e5df8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0010817-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "08a27a81-561d-41f1-9d99-6266c1f230c9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "65645e51-3cea-4c45-a029-ecd7cef6c8ad" ; + crdch:id "f3270d37-2d06-4867-973e-54e8ea28208b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-001639-6186_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0002787-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b1a851b3-94bf-4652-82d3-cc6133cd1565" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3eb1f15d-003c-42bc-8832-ea364ee8931b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -17069,89 +16203,128 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ea23b8a9-c2fd-5392-8625-a26662cdf0ef" ; + crdch:id "fb0593eb-d74f-436d-9bc3-37f8d8285296" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7404_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-009648-9028_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a39131b9-e7c7-4385-a1b9-d8a0a0950337" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3c02ad20-11ec-4e71-b7e8-c29194ae502f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "0be93ffc-ad62-42bb-892a-ba10c4da6f39" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0017332-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:20:07.713564-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a0723862-62f9-4770-b415-e8f52c447e7a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "43637316-5d63-491d-b4cd-2caa045d8c7d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "05282f77-9656-428f-9517-9edc96cb7360" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0007543-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "025ae6c3-bdbe-4db0-ac71-56df7e80ea0d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "27fbdde4-c58a-46d7-a96f-918b64fe5b51" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-037700-159036_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:26:11.717995-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "50b8e07c-b892-4fac-bf59-9e093e2d74d3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "a1439fe2-31b2-4a31-973f-fbeeb13a965f" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "530535a6-b47e-48ce-b312-54c3003c14ad" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0001405-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0002854-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5dcad3f6-29d1-4043-8bf8-c8ceb17c5ec4" ; + crdch:id "ad472d22-bccd-401b-ab2d-0ab7a31c7b73" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -17165,9 +16338,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bb2f0211-8bd8-5667-a49f-0e507f10e863" ; + crdch:id "b588dad7-169a-5ecf-885b-580be11d01cb" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7424_diagnosis" ] ; + crdch:value "TCGA-CN-6992_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -17177,14 +16350,14 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9308d3df-4126-470f-9dae-db9362050c29" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "ce0b9c55-baeb-4ca8-9235-51a836a4b58f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "162ba21b-8262-4815-9e65-5b064f0e5885" ; + crdch:id "7a5921a4-5714-44e7-8ebd-048031b32b88" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -17192,86 +16365,79 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "979324ca-d8fa-4bbd-ad7e-1c663c5a4a9b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7dafe515-fefb-4656-ab96-b72e09e041f7" ; + crdch:id "b86352a7-2987-4743-aa3c-1895c438641a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f068b7ad-5b43-44f0-95b3-33ead995b8cb" ; + crdch:id "dcc6b724-3a6f-43bc-9a7a-eb031a031212" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010161-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0000433-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ea42167d-71c9-4eda-8153-2b207208d97d" ; + crdch:id "afcf4bae-7e95-4306-9627-c9a9d6011dfa" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -17285,20 +16451,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e1518a49-5ef2-41ca-ac88-edc88e8ec241" ; + crdch:id "c652d5fb-652f-485c-99cd-4e3e00af1126" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-e8aa0080-sample-a_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0000396-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "baf6aa81-4b32-4d7f-8557-5942a0febb91" ; + crdch:id "2bde1811-da29-46e9-973a-45ea43387818" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -17312,20 +16478,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6307ff41-9bb5-438d-8789-a73b41303d64" ; + crdch:id "25fb47b9-2f00-4140-92bc-462b1e8447c4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-036509-75021_diagnosis" ] ; + crdch:value "GENIE-GRCC-4wf609jo-sample-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-27T19:26:40.896040-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ba40b824-5fe9-4a73-b7f0-9b371af64f65" ; + crdch:id "0ef8dcd6-8f67-4f29-a69d-d952df3d43b3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -17339,23 +16505,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "e071dcbc-10af-49bd-86cb-b1c8ec549487" ; + crdch:id "d75594bb-d5e3-496f-b1c9-1743ae942c53" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0017414-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-DFCI-008027-5967_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:20:07.713564-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ff1a3e50-533b-4228-a8fb-93af76ca4b59" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "f0afc508-eff1-4a28-b912-3705a87d607d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -17366,23 +16532,116 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c5df4db4-06f3-4596-98d2-3ab0e5df45b6" ; + crdch:id "bb2f0211-8bd8-5667-a49f-0e507f10e863" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003711-T01-IM5_diagnosis" ] ; + crdch:value "TCGA-CV-7424_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "162ba21b-8262-4815-9e65-5b064f0e5885" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7dafe515-fefb-4656-ab96-b72e09e041f7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "979324ca-d8fa-4bbd-ad7e-1c663c5a4a9b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "9308d3df-4126-470f-9dae-db9362050c29" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "3f8fca8c-e8c8-4032-a0ac-488e49fd623d" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-023359-23864_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7eef7c3e-d42d-4cf5-9ad1-3099b828f776" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "9eb7cb20-106f-4668-9ef4-c0344e8df3c1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -17393,131 +16652,113 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "18cabf3d-233d-5ad2-a5d3-a2a10677c99a" ; + crdch:id "a276fc76-237c-5574-9fc6-4b309ce35829" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A4II_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-6935_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a76bfc3e-fa46-4a65-88e7-c644c8b20098" ; + crdch:id "6883e88c-05a5-4ae7-a43f-40d4f35a3a2d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "05aa5c47-cbde-491e-b8d7-a60cfe1ca2d9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "81bbc439-0c8c-4d39-bef2-03901b31c50e" ; + crdch:id "76de8a78-90b8-4928-8dc1-bf3b8157382f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "37f4a944-d427-4f41-9d27-982a910103e8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; - crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cf507905-7cf2-408b-a08e-b703df54147f" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-NKI-DYRQ-CX3U_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "36b762ea-ade4-4e7a-b824-0fdadd0e33ef" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f9e5f978-310f-4011-86bd-f468da998bd3" ; + crdch:id "fa79bd3b-f6c7-48c1-93af-5b6fb08de876" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015030-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-DFCI-003292-1283_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:42:39.927651-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e3362d03-8d6c-4be0-b1a6-5ce9c230f4f0" ; + crdch:id "a3eaae17-ef1a-442c-93cc-0fd82a8887bf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -17528,59 +16769,44 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Basaloid squamous cell carcinoma" ] ; - crdch:id "b4c1dd26-92ca-5bf7-b861-bff7f68e8436" ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "424f3fdd-09f1-57a2-99de-10c13b9be653" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A6SW_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-D6-A6EP_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; crdch:system "GDC" ] ; - crdch:text "8083/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0b1a1f48-c58d-447a-be06-1f4e0c1c39d2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "1e8ad4ff-09db-44f6-9527-b10ac22453d6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "dc6d258a-dba3-4186-bf89-9efb70a32365" ; + crdch:id "434adba3-549a-45f7-b89b-76737678ae0e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "50e494e8-d48a-44ec-91b3-5755b42f70ee" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "661cafd9-0cf9-4c6f-b541-293bdecf3ede" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; @@ -17592,67 +16818,55 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N3" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Adenocarcinoma, NOS" ] ; - crdch:id "25182ec3-0d7b-44ca-82e4-f1a8d7de4a28" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD18004_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; - crdch:system "GDC" ] ; - crdch:text "8140/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:58:46.365657-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b62fca52-48c3-4bea-b5f7-5794a1ed4f43" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iii" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a276fc76-237c-5574-9fc6-4b309ce35829" ; + crdch:id "f29e70db-e331-5bcb-82fc-f2e15cad5985" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-6935_diagnosis" ] ; + crdch:value "TCGA-CV-7433_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -17662,53 +16876,34 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6883e88c-05a5-4ae7-a43f-40d4f35a3a2d" ; + crdch:id "5c4960e6-92f7-4576-a7d8-82a7c3d7cd5f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "76de8a78-90b8-4928-8dc1-bf3b8157382f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "37f4a944-d427-4f41-9d27-982a910103e8" ; + crdch:id "c2530f39-c334-4a38-b75b-b74d5cb95920" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "05aa5c47-cbde-491e-b8d7-a60cfe1ca2d9" ; + crdch:id "2916fc1e-ba62-4494-8014-dfcc6dd358ea" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -17718,21 +16913,33 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; @@ -17743,357 +16950,290 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a433a5fa-fd34-4ab5-a117-29614a2c7f9a" ; + crdch:id "c1cb359f-50c5-527d-941f-328d1d34f062" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0013513-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-IQ-7630_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3b35e7e6-0e30-48be-9d22-d95fb49f1227" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d81234fd-4e10-469a-81e6-f23a192f1ef1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f2ec974c-b952-4450-947b-11c39bbaf248" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "bd97a61f-6744-455f-88cf-2a418f2458a0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "bbbf3549-d0cf-4dcc-bc92-32d12cd2c96b" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD10083_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:54:12.244834-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "712ad6f8-8c2a-4c82-a89a-10ff849e3e9e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1f6860df-38fb-5519-8ec9-3068b0476cf2" ; + crdch:id "83e6c6d4-83d7-55d8-ab82-aba8f3e543f5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4735_diagnosis" ] ; + crdch:value "TCGA-CN-6988_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "feb21d9d-394f-402d-8659-eb15bb95f0db" ; + crdch:id "ca2a45b4-1eb0-4e28-a4c8-5647bfbaa98c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fbb300fa-8793-42da-a68e-4570ae2e5186" ; + crdch:id "4f72ee1e-37e2-4845-90de-812686a25980" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a2caeab5-55a4-412f-a647-0112f48bbbe7" ; + crdch:id "5bf33753-d3c4-4fbe-a8e0-af958efb6fd1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4f08ca0e-bd9c-425c-9137-a8bc3654ff09" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0004619-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "407047a0-1065-4e67-aee6-a3a66998deb8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "eaa3ca60-5565-429d-8c4b-a0a6ef7d9fa6" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003114-1605_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "9e503ae6-5765-4fe6-9a28-eac5a3a93a13" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "48e8dd81-ed4d-5c54-af66-84e86477d5c8" ; + crdch:text "Basaloid squamous cell carcinoma" ] ; + crdch:id "fd9653a3-00f4-593c-a8e5-81ed124ee898" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A6DL_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-QK-AA3J_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8083/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bd90f967-84dd-48cd-aec0-9de9a76df7a9" ; + crdch:id "b67c34c3-8e4e-41cc-865d-43ee8c9d3d78" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "256469d0-5f36-4966-bf4f-3b4297e55f43" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "dc102dcf-3f48-49e2-8a6f-cfdc34f8ed0f" ; + crdch:id "410b2727-8446-41b1-92b9-42671d118a39" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "6d2f2d82-2fa5-44ea-a714-85c05b5bd255" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "Stage I" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T0" ; - crdch:system "GDC" ] ; - crdch:text "T0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3adce70b-ce30-4b21-beeb-2a7bda73ca3d" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008134-5168_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "37b86231-4224-4084-a523-800e98c4fea3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "stage i" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5a82f834-a2f8-4d61-a816-c410213556b4" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000319-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d0ef535c-d0ed-471d-a1a6-3cf9600d37cb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "12b8aa2a-5f0f-4d64-9cc0-ff4a65619c10" ; + crdch:id "fbf35ed3-c5af-4591-88be-e9971b7d40f6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003438-7875_diagnosis" ] ; + crdch:value "GENIE-DFCI-053418-203556_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:20:30.865187-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8ccd1ad3-a277-468d-ae44-03e6c1964c3d" ; + crdch:id "a3b9c3f7-8499-4c17-92f9-274b1ee52764" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -18107,19 +17247,26 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "73fd5157-4aa2-5b2e-852b-889d058a6f8f" ; + crdch:id "5baa4771-eb6d-56d1-821a-33157bf79573" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5366_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-BB-7866_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "62fdf8f3-a028-453f-b27c-c2506be68cbe" ; + crdch:id "fb5ba525-1658-4f8b-81f8-8d7ec3727773" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "736c3c8c-ff9f-4892-860f-04665a1f344b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -18127,132 +17274,154 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f3e5a16f-7c16-425e-8321-b6b19fd469d3" ; + crdch:id "af5d22cc-87f4-4b91-97bc-7103bc07adcc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "111ad944-f78e-4ec6-967b-f05c49b49b1c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "N1" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6d395db6-3f58-4c4a-82dd-9b3b9c35fc8f" ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "8d12f0ed-6345-50f9-aad6-68ae3ab8dbb1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004670-873_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-RS-A6TP_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3396e2a0-10bb-43b3-b5be-7980064889e0" ; + crdch:id "5d166131-946a-46de-b446-ea35d8b0e1a4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c34f7850-ab91-4173-b716-b487c290ec78" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0012862-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Not Reported" ] ; + crdch:id "281693cb-2d6f-4a42-af26-d807ea67a191" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "59d43c02-f731-4a7f-97ae-c3d7dac2d5e0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "1ce08042-34c7-450e-b1f5-8cdf9bfc5a77" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cbdf0116-28d4-42a0-ba6e-43a8587de68f" ; + crdch:id "47d4038e-908a-40b8-8a91-7bdcc4421624" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008605-9620_diagnosis" ] ; + crdch:value "GENIE-DFCI-007857-7172_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; @@ -18263,7 +17432,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "faf18ba4-6d92-4da3-bd43-5071bb88c5e1" ; + crdch:id "01a0cb84-c716-4134-aa16-ef008ae30469" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -18277,268 +17446,142 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d957f533-9896-5f0b-a9ee-90335d733f67" ; + crdch:id "2fcaff59-bc46-4971-9a75-dcbf2c85a5ca" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-7864_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0013498-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1477b393-8acf-4550-86a7-6570c0d7d583" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f3c568ae-ad12-4155-a652-8e16e5276bda" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "4775330f-0409-4bb2-a096-a3d1eb0180d1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "1c156e43-c8c3-4ecb-83ff-2075ebd89cd7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "eac797ee-ffad-5c80-8f0a-7e95590e118d" ; + crdch:id "0b151db5-f3df-4cc8-9bf3-049308634116" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7389_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0001794-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9c35c1ec-5ca6-4900-aa39-ab1c962b9c4d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "2da79fb4-bd1b-4518-a6a2-6159251d65fb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; + crdch:system "GDC" ] ; + crdch:text "Malignant rhabdoid tumor" ] ; + crdch:id "2e79ab38-e511-5e60-8c81-1584d28a909e" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TARGET-52-PASVDP_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:system "GDC" ] ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:system "GDC" ] ; + crdch:text "8963/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6e926ab9-e086-48cb-876d-d490c46cb7f0" ; + crdch:id "a28e1682-4703-527b-bd4e-81f86fa6f35a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Blood Derived Normal" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "fd9ff1de-6856-5a42-ad32-2e3aa28dc2d7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ] ] . + crdch:text "unknown" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "26ffab97-fa9a-5135-b283-8c4aebe51a26" ; + crdch:id "60d7b883-bf64-4777-9f6a-efaf4c4a40c4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7250_diagnosis" ] ; + crdch:value "GENIE-DFCI-003875-1298_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3e6bc216-301a-4f24-911c-8c3610e4a015" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "6f55766a-d980-414a-be4a-369e93ec3436" ; + crdch:id "c930148f-2059-480b-960a-4efcb3c98ac1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b4f8ddc9-0ab4-447e-8292-5dcf8a9085ee" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f5472b70-32c8-48b0-9051-f9b33272ffd6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "43aa2ba4-d59e-4e9f-9b1f-009fba8ee08a" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "d55686fe-0423-4b01-9719-ade00bed3004" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-4754-15863_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0009761-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c3431e69-82eb-4eef-9e13-312bfde95103" ; + crdch:id "64dd4e81-f01b-4846-b306-20b7cd7d9340" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -18552,23 +17595,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a4332fc7-aee9-497b-99ba-5c1d548a7623" ; + crdch:id "f14b2d60-39ff-428e-bfb9-a33f4d3242ee" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037277-88571_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0002193-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d2ad484e-58b3-4e29-84e3-a45abb294b3a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "f2f48558-d331-431f-a14d-845efe0c6ce9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -18576,209 +17619,82 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Basaloid squamous cell carcinoma" ] ; - crdch:id "f4e541cc-a71e-55b3-ad08-3eeb8d00f2b0" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "cae73de1-65ae-48fb-a08c-355e6921dca5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-KU-A66S_diagnosis" ] ; + crdch:value "GENIE-DFCI-006462-4354_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8083/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3c09f5ba-a4af-4384-948a-d6e943613f7a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "4bed3ece-2350-4c99-bec9-3d652fbe8c9b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "a590a632-55b4-4be6-b2d8-6c8afbbe99ac" ; + crdch:id "f632701a-5242-4839-b96d-0214c7e9a73e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "8723983c-94ff-55df-8165-6fd5937b5462" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "68a8cfd1-e890-4bd7-931b-33636e8cf10b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A63T_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0000668-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b477dfb8-c039-49d5-9a0e-912946dc3ad1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "75c0a7b6-3e82-4ce9-8856-dd3475affe87" ; + crdch:id "5c9ff077-5620-4611-a58c-fdd8ed98b2db" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "74606f8c-46a7-453e-acfd-91203aec6df7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "a099ae58-fa38-4a90-82b6-c97a23b317f0" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "533bd04a-5e63-4ae1-a929-487ae3597956" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-f88a03a6-metastasis-a_diagnosis" ] ; + crdch:value "AD5852_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:25.573239-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a9b18808-3ee9-4274-9a83-8d2fcbc16c7f" ; + crdch:id "f7b249aa-b35a-4e08-87b6-e9a79d75edbd" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -18787,23 +17703,23 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0b96cae3-d332-4e5e-ba59-e0a6bc6573df" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "a2cd4aae-5655-4082-956c-f5bbc733c576" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0017105-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-UHN-221761-ARC1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:17:41.081467-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ba279369-073d-4976-8439-3a318c0f0fc3" ; + crdch:id "5103a1f3-d342-462e-9845-9703579d26f8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -18817,103 +17733,114 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ce208b92-611f-5ffc-8a6f-b01b91e7b58b" ; + crdch:id "1fa242e0-09fa-5f9b-b6ec-b07d25fd21cd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6474_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-P3-A6SX_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ddad5854-74a2-4db5-94d1-41196a37be5e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "cc710f34-9fb5-4474-84df-5427b59aa062" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d84c30b6-e217-4b2c-9dc1-16428264378d" ; + crdch:id "65b091e0-fd47-4f4c-87f1-b2ba9c2766c5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ae3f666a-0c18-41c1-b00e-90cd85a2f987" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fb0593eb-d74f-436d-9bc3-37f8d8285296" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "f1143020-2e95-4028-a2bf-c03a5ba6ea4e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009648-9028_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD14041_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:41:38.922504-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3c02ad20-11ec-4e71-b7e8-c29194ae502f" ; + crdch:id "fe72277e-ae77-486d-b5a9-844c483267eb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -18925,9 +17852,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c0dca6b0-81eb-598e-9514-f23513df1ab8" ; + crdch:id "c2494ea4-5db2-5716-9afd-096e152b592c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A71D_diagnosis" ] ; + crdch:value "TCGA-CN-5356_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -18938,156 +17865,96 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "87d8fec9-7ac3-4359-a6be-de270584ac1b" ; + crdch:id "fb9d2ba0-7673-4587-ab69-0059fce2f671" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e4157201-93f3-4f08-b3a9-dacb22671a57" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "bcb5da85-78d6-4519-9740-378587b1bd37" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "297ea792-1a29-44db-a14b-38513b50826f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "cf684788-d8e6-49da-8421-b2dbf040a529" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; + crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "49934fcd-822a-4e1f-ab12-46ef9216779d" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0009754-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7c2babfc-9948-4332-8c28-096971073c2e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0b894a71-55ca-4246-bdf3-4d36622b203c" ; + crdch:id "5db2900f-3088-48fa-ad1c-8dbba6bedbef" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0007622-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0017777-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "8b9e009a-6ead-4105-a148-8c8a44be0658" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "2326f9b7-e2e8-487a-acd4-b00bc9967a8e" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-6597-17790_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:37:32.909734-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "35f0c152-0c87-42bb-a1b7-b306e66514f5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "dc326cf0-cb20-4f0a-968a-28c6923319dd" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -19098,20 +17965,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "770f08b4-6ea7-4cb0-a423-75909447e60c" ; + crdch:id "53ddd4d3-8e0e-4e6f-9cd1-fe6c9c5eb114" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-518360-unk-1_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0006525-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-04T13:56:37.232985-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:02:01.981535-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "75fdf08c-00e0-42dd-a21c-62cceb7bf00f" ; + crdch:id "379984ec-2e8f-4c3e-9153-1ec8adc17770" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -19122,156 +17989,201 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "8d12f0ed-6345-50f9-aad6-68ae3ab8dbb1" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "dac87ff6-12f3-553f-a6cb-fae679002ff0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-RS-A6TP_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CN-4722_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "281693cb-2d6f-4a42-af26-d807ea67a191" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "60c8633c-16f9-4066-8aad-311b04b935e5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1ce08042-34c7-450e-b1f5-8cdf9bfc5a77" ; + crdch:id "6e767fc9-0f5a-49ec-999a-cda2daeba6ff" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5d166131-946a-46de-b446-ea35d8b0e1a4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "47e7b839-bde5-4b66-98da-7ed6e3e7c29b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; + crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ] ] . + crdch:text "M0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Malignant rhabdoid tumor" ] ; - crdch:id "33c5c040-da3f-5e5f-8d13-ab9eff88f833" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f7be786a-80e5-5c78-af12-715c8cdd318f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TARGET-52-PASCDH_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "TCGA-UF-A718_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8963/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "da724216-c1fe-5420-9e73-3a9d4b52bf1c" ; + crdch:id "ddeeb19e-1929-488d-8e19-c6212b3b78fb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Not Reported" ] ; + crdch:id "8f620b3e-2962-49da-bcaf-4ecfd9580923" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1d3eef26-a725-51f7-95fa-139d1a7da76e" ; + crdch:id "a88696d9-b36a-4fd7-b3ed-b6b31aa4094f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "unknown" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "309da786-ca2c-4c3a-8907-5e690f375f54" ; + crdch:id "6fdc7de3-3d2e-459a-94ea-1dba9572f47d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0008800-T02-IM5_diagnosis" ] ; + crdch:value "GENIE-VICC-480293-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5dec4e0d-afbd-4ad6-8acc-00b5ad113a03" ; + crdch:id "116b69cf-c9f3-45c6-be86-c4f22a36dcf8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -19282,112 +18194,103 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "28f3f8b9-df0c-5c03-8414-89640fa631c5" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f0a3480b-d52a-5db1-b03f-693a9bad5cfc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-H7-A76A_diagnosis" ] ; + crdch:value "TCGA-BA-5559_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "452e53e7-b219-4ba7-b8ab-870e1ba4423b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "43fbb037-8ba4-4ba3-8458-71a027eda822" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "148ec5a3-19ed-4949-bf37-9bc4e6203966" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "8c925c97-a7e0-44b3-ac62-b365e89975f0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "78229167-1f08-416d-be98-74f757610349" ; + crdch:id "fbea64f9-b46b-4af1-bfb2-1791d93977b6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; + crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ] ] . + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "6f840d0f-a369-413c-baf1-35200313c274" ; + crdch:id "99aab93f-633d-4ce6-8ccf-36cb05c5d2cc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-a679ee35-sample-a_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0007575-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "60e15dc9-5d8b-4104-b6c3-bc0b7b3109a5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b1d7b582-2302-44fb-a98f-13372ca17247" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -19398,20 +18301,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5ba2b63c-b0c8-4304-820c-9b04ebb5a7fc" ; + crdch:id "bcef8cad-3d18-4cd2-b839-5fddd16311f1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-002837-2078_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0000945-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fb20acec-aeb5-4591-b114-0834c6629db7" ; + crdch:id "2ba57cf3-fd06-4f99-9ad7-447a164b9586" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -19422,25 +18325,58 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "05282f77-9656-428f-9517-9edc96cb7360" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "db8fb969-2213-4290-94de-c3680cd314f7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0007543-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD16283_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:28.078592-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "025ae6c3-bdbe-4db0-ac71-56df7e80ea0d" ; + crdch:id "0d4e791a-4a50-4c58-a8a5-88e5bf4d7c9c" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "b0179bcd-bda0-42ff-8654-61f3fe576e73" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD12050_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:03:00.815411-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "0a8dd963-c724-4a77-b662-5f711ac88607" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -19452,23 +18388,26 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "09912911-2865-490c-aaca-89f4cc1bee36" ; + crdch:id "c70dbc51-07bb-49a1-bffc-ea639cf09e66" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008390-5815_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD5893_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:40:08.863452-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7894955b-ac0e-46ee-a5b3-c023cd1e87b6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "3c1903f3-2a52-46cf-872e-060ba3a092e3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -19479,47 +18418,160 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "1d93a53e-6030-43c7-b479-9faa6fc8febf" ; + crdch:id "11781aec-74e7-44bc-86ce-9941aa62b6f7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-002633-5917_diagnosis" ] ; + crdch:value "GENIE-MDA-1594-3307_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:00:11.934564-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a8ec3306-0190-4e13-94d1-e269b8479a1d" ; + crdch:id "4cb8fa37-e3cd-4d7e-bb34-67ffdf228d78" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "73adb3fc-a3c9-487c-a0d0-fa8b09707932" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-005121-1375_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "eadf6e9a-c6c3-444c-8e93-8ab77ed87d09" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "b7c8a51e-1403-54ce-a94e-ca7cfc05c21b" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-HD-7754_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "adb496a1-07eb-45b9-8690-00184143300e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-23T13:20:20.149518-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "97d5f4b1-b8a5-4fb1-8af6-f0e6cfc302f6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "3fb86c71-0f8b-4022-b19f-d394401df9fe" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fb2076bc-c2ef-4566-ab26-c6c6fcd212ed" ; + crdch:id "cb7a6350-80e2-4b6e-9b86-05632255db52" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-b3db0c02-sample-a_diagnosis" ] ; + crdch:value "GENIE-DFCI-003213-4767_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "01b01d59-07d3-481d-b466-bf77a916a0db" ; + crdch:id "a764b89e-ad60-4316-a812-24a5eec7b9dd" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -19530,25 +18582,28 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "99aa5d5b-c650-47f5-b485-da3d78661529" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "ce0e772c-45e6-4686-9db5-f88e05e2f713" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0018925-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD12118_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:42:00.849990-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:00:58.377064-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5007e321-c75c-45c2-b4a7-0d3cbde5280a" ; + crdch:id "fb315485-9a4d-42a8-8e1b-8cc97c708f1d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -19560,9 +18615,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c18fbc5a-880d-5f56-8466-527763c437d6" ; + crdch:id "becd7cb0-9352-5c38-856c-fcfa539fdea3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A45Z_diagnosis" ] ; + crdch:value "TCGA-CV-5431_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -19573,93 +18628,96 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "866bc103-c5bc-4365-8ef6-40064b33046d" ; + crdch:id "8897e2b3-1863-43c7-a84f-fe53d12371f9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f844574a-cb7f-4f66-83d4-ee0ca41a63d1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "39e3facf-6d13-4611-bcfa-90ef0350814d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Solid Tissue Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fc3d6178-acc8-4e4f-b935-3cc1f6c0f304" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "be567c0a-3833-45d7-b846-d229a8e16e16" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "8bc744c9-1120-41c6-a782-3bda1bbfa2ce" ; + crdch:id "274578bf-55cd-4807-9c8e-573db026da1d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0012578-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0002592-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:17:29.664139-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "31be6816-e615-4939-8c64-c523db6a438e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "a75ac689-6228-4806-b699-874f8ec28ae1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -19670,20 +18728,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d7d13cee-ba1b-4e36-a0a5-3f925c871020" ; + crdch:id "c1551a30-c8b7-4ba5-b5ed-044b55587a38" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0013833-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-003078-318_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b6ddcf15-8ecb-47ca-bb29-60b9b43fa7aa" ; + crdch:id "1647be39-e387-4457-a1c0-83483d25ea5e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -19697,133 +18755,109 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c0bf8ccd-6f3b-5ede-b3ce-a63ad584ab1b" ; + crdch:id "7747a88f-1a9b-5833-9442-af0b1350bb4f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-DQ-7595_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CN-6013_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Gum" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "387e8df2-f053-4cbe-aae8-5727d215f904" ; + crdch:id "8b510bc8-7b3c-4861-9a40-c2c30b7099e0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c522234a-c0b1-427a-8992-84fcfc9389ef" ; + crdch:id "c0c84016-117e-498c-9ed9-52e279e89e33" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "52e0aaf1-d93b-42f8-b0e3-f6b4a3d0bd1e" ; + crdch:id "d018cd44-6b01-44f2-9181-81153225aab8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0099f9fb-0d9a-46a0-a86f-c10dd58ad440" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD8066_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:51:17.672127-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "dc97ccf6-b026-45ac-a658-fb44806230a1" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "T4a" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "dcc6b724-3a6f-43bc-9a7a-eb031a031212" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "00fbc722-7387-437d-b859-3d35c86e02fc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000433-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-040b2fef-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "afcf4bae-7e95-4306-9627-c9a9d6011dfa" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "25007740-c3ea-41f0-a9dc-52de44cb9faa" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Not Reported" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -19834,49 +18868,52 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1fa242e0-09fa-5f9b-b6ec-b07d25fd21cd" ; + crdch:id "2b3b0e72-0926-5ed2-89c8-ffa1585d111f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A6SX_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CV-A6K1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ae3f666a-0c18-41c1-b00e-90cd85a2f987" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "43115789-cca5-4dc0-8377-e47b90c3f16f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cc710f34-9fb5-4474-84df-5427b59aa062" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "09b49e67-34d8-496e-b42a-5123fb516cc0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "65b091e0-fd47-4f4c-87f1-b2ba9c2766c5" ; + crdch:id "8ae503f5-a283-4bdf-8c82-de63f534bc85" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -19886,119 +18923,209 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "N0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Basaloid squamous cell carcinoma" ] ; - crdch:id "fd9653a3-00f4-593c-a8e5-81ed124ee898" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "b8812861-0e19-58f0-bccf-667970cdb04c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-AA3J_diagnosis" ] ; + crdch:value "TCGA-CR-7399_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8083/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6d2f2d82-2fa5-44ea-a714-85c05b5bd255" ; + crdch:id "3dd4255a-7359-4b51-8a0b-44d9e249956b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b67c34c3-8e4e-41cc-865d-43ee8c9d3d78" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "410b2727-8446-41b1-92b9-42671d118a39" ; + crdch:id "05c3d8a0-47a2-44b2-b0c3-144ec0cb2673" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ], + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "T4a" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "37ac68db-02ec-42d2-92bc-d7d2f4c33bf8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-008078-6166_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f2c471a5-55a3-4180-be7d-c3560efade4b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "8764fb2b-e701-53db-b137-03efa2c52637" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-BA-A6DI_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:system "GDC" ] ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e7a7e296-3f1b-49f5-bbaa-082f918d080d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7b56068d-21e9-4879-b747-c99943e40e50" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b0d4b16c-cc81-405f-83a1-de57cb488166" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; @@ -20008,80 +19135,89 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "bd9d72bf-8331-5bd7-a4bc-1522518d3fb7" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "cf36baf2-10e8-523f-9dd9-0f9c938be574" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A468_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "TCGA-BB-4223_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "54fda578-dfb1-4a1b-8b01-2b7e9292f387" ; + crdch:id "82db742d-885d-4788-b509-474715ae183b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7dc1e99f-c601-48c2-8326-389d9f084e29" ; + crdch:id "3285f0ab-61e2-4235-b0ac-af1718ca1874" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "66643338-ed21-460e-a1dc-b547c5b14500" ; + crdch:id "75430612-09bb-4d6f-9304-62a5b517d424" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; + crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; @@ -20094,19 +19230,25 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "693a7e67-099e-5382-b7e2-e70d6d15406f" ; + crdch:id "51ca5228-56c7-5d68-9285-1bbfbe8b4492" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-6962_diagnosis" ] ; + crdch:value "TCGA-CR-7370_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -20116,90 +19258,66 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5b2faa3f-c96e-42c6-81ce-a356852ea6a6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "70b5b27d-3905-40de-8b70-9185cfc49d94" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "366f8ab0-ddd8-4383-9bc1-96ef342b749c" ; + crdch:id "0e357973-d52d-4fc7-8099-7b87458745e2" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "73d79c62-61b6-4e72-bc8d-c3fa2a344caf" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "339524bc-bc1f-403c-a12f-6e8ce72fba50" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c8b3a37f-01ec-481e-9460-0bcac22cc002" ; + crdch:id "2707217b-5a4b-404b-97de-921526581d45" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-18076aef-sample-a_diagnosis" ] ; + crdch:value "GENIE-GRCC-2b4655c3-sample-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; @@ -20210,39 +19328,114 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "960fe012-e237-42c8-a3e0-d02853ce3818" ; + crdch:id "56e9e0e1-5435-4b6b-93a0-70564fe1aa27" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "4679b4bd-c891-5a60-9b12-1e6bf1bb7675" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-BA-A4IF_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:system "GDC" ] ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7bfdae74-2bf4-4ec7-b08c-acd9b9e0baf4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5eea7c58-96b4-426b-9685-15599e534730" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "130676ad-54bc-4d20-9ec5-129d4688296d" ; + crdch:id "dc412cff-36a3-4721-b1f3-8e16ed74489d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD1478_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0001186-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:54:59.697804-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "50977953-c3a2-4b71-b40a-3f211a269cc5" ; + crdch:id "1853a05a-8846-4da3-9509-bff587eb6e8d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -20254,23 +19447,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, NOS" ] ; - crdch:id "d8e6b6ed-5c11-4a78-b25a-07f23305bb40" ; + crdch:id "6f1ab30c-67b7-4a7f-b4ef-22b1221bec7d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-6285-17334_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0012422-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:17:29.664139-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8479ff0a-fce8-4f4e-8d00-6775d1e9cb00" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "e125a436-ca27-4a85-bd9d-9ca108306229" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -20281,20 +19474,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "6176f8de-0835-4f23-9ce1-85511ac4e1f9" ; + crdch:id "fe440219-2351-41cb-a0d1-e22bc73d4aa0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD7774_diagnosis" ] ; + crdch:value "AD941_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:50:23.633804-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:46:27.877516-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bcecf093-e764-4c32-81e5-619d0e86216e" ; + crdch:id "5e91c356-4431-478f-8033-99442bcdcb95" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -20311,70 +19504,106 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a3c1a290-626e-5e1a-b120-0153a79fadd1" ; + crdch:id "8bd7b118-92b1-4443-8753-f779c82ef116" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4741_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "GENIE-DFCI-035615-74950_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-27T19:26:40.896040-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "151f2c1e-f448-4fa5-9b61-81dc5c339f58" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "bddca644-5ced-5789-8d31-c00df9f776ad" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-D6-A74Q_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:system "GDC" ] ; + crdch:text "8071/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8d8ddca2-6461-4a8b-a696-da0906661b9e" ; + crdch:id "343c1ea3-2785-465f-b01a-2d609b486ef9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a47974a3-b37e-4041-8953-5f50f8745681" ; + crdch:id "c03b3dfa-7b9b-4a21-9274-d174bc14440b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "03c9108a-5139-4bac-9641-c7dbbedef420" ; + crdch:id "d9095c8b-414f-41d4-a478-ee54d2728762" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], @@ -20389,58 +19618,165 @@ crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "b8f93296-f293-4af4-83bd-6ae35aebe59c" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-010368-9817_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "094236a4-db5d-4e05-b020-5136ee6f4225" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c508644c-d496-4647-a065-4e0077d99b67" ; + crdch:id "e68bc170-6152-4c90-9b9b-e31856495716" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008357-5599_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0005506-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "80c31730-c365-4f43-ae30-d082f4c7f67a" ; + crdch:id "b5f4b393-678a-4964-b625-19c8099cde13" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "28f3f8b9-df0c-5c03-8414-89640fa631c5" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-H7-A76A_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:system "GDC" ] ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "148ec5a3-19ed-4949-bf37-9bc4e6203966" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "78229167-1f08-416d-be98-74f757610349" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "452e53e7-b219-4ba7-b8ab-870e1ba4423b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "562417d9-1094-45a9-9621-7fc5ce203ac3" ; + crdch:id "8a0ce16a-46ec-433a-9679-e76ca74240fc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD2564_diagnosis" ] ; + crdch:value "AD5506_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:00:26.233095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:41:09.015209-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4448e3e1-aeff-4ea0-82e4-1692b9b59414" ; + crdch:id "14f00898-8aaa-4008-9eac-0959333c3525" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -20454,210 +19790,294 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "95d85e5a-b82c-59f8-b7ad-710e019cdebc" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "e89ecbde-44e3-5db5-be20-af6cddaa4e92" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-TN-A7HL_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-T2-A6X2_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Gum" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9c02fd4a-a29a-4a44-ba96-5acb6ff11f7f" ; + crdch:id "fe1541c0-a239-428f-bf43-8b8b999d362e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1077bf93-cf23-41db-925c-c633921894cc" ; + crdch:id "0080b5ac-b9b2-4fef-ae51-6a6178325364" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4a0d79fe-9eb9-456c-b483-ccf956597a3d" ; + crdch:id "161b6a0e-0b50-41a1-bdf3-bd7666067454" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "Stage III" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7bbdbf5a-baf7-55b4-bd8d-89e213744a26" ; + crdch:id "f44a9ab8-f121-59c5-8087-567864266629" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A6VC_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-CN-A63Y_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "76240522-a39e-48c7-80e0-241277fdb705" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "50cca7c4-4586-43cd-a59e-3fdc646f5aba" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d278f388-2a5f-407f-886d-961272ca28eb" ; + crdch:id "daaeaef7-3f0f-4155-908d-9aa6e536f94c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "dbea2268-ac62-4ab7-aa7d-86f029fcb2df" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "e0b45d74-3b6e-424f-86e7-2174d7c1245a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "stage ii" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "9be1751f-17dd-5748-a489-1b4eb3235e17" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-MZ-A5BI_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "c226c7c5-64e6-4790-a420-c2f4e0196453" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f1e46036-7b4f-4cca-a150-f2d8e599fdf7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "576b4319-20fe-4dd8-82b1-c34a70bd2182" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f0b5d732-2466-4d9a-90cb-ec3084606849" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0010677-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T19:11:18.668081-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e084b5e5-05ac-4229-bbe8-f640f231e1fb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6d9a9668-da18-4c45-a108-8b0b058ec47c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-596e5ce8-metastasis-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-006284-4777_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7889cf51-be9b-4193-b057-5f348fca10db" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "6b2d8256-f78a-4ac8-b0c3-a97a03410b59" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -20665,53 +20085,50 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Malignant rhabdoid tumor" ] ; - crdch:id "cbc897af-ab20-50cf-b397-5bdaeadb4691" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "ca8f5806-a2af-45ee-8217-e6dfc4d0b229" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TARGET-52-PASAMZ_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "GENIE-MSK-P-0012391-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8963/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:17:29.664139-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e5a4af40-c272-5aeb-942c-4be4614b4cfd" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:id "3c8fe733-1711-4d4a-a64c-b94788eda279" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "unknown" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "53ddd4d3-8e0e-4e6f-9cd1-fe6c9c5eb114" ; + crdch:id "b0f16df9-9556-4ff1-b8b8-afabece2fd14" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0006525-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-UHN-071596-ARC1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:02:01.981535-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "379984ec-2e8f-4c3e-9153-1ec8adc17770" ; + crdch:id "5cdc6f40-9b5f-4dc0-9082-a9500c3e5af4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -20725,9 +20142,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9808f3d0-16f0-519d-8e0a-9061968bc749" ; + crdch:id "2dd60fd1-68e1-519b-af66-00c32d0cb6d4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6023_diagnosis" ] ; + crdch:value "TCGA-QK-A8ZB_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -20738,95 +20155,125 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0bc27973-621c-4011-bcbd-3b7f3464389e" ; + crdch:id "44c64654-0e37-4c13-b4fa-aaf9c6644445" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5e42be68-8865-4c69-8684-0f6e5c6c9b94" ; + crdch:id "17a0a479-3b48-4852-ab06-dd33d6f7788a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ae1a6096-8d51-482a-8c44-cbfdc7dd6458" ; + crdch:id "936a8a93-6559-4bf8-9c51-e81ec4f2aff7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2c" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6ea3680f-baf2-53a3-8308-ae9dfd6ceb1e" ; + crdch:id "cb8fb063-f8b5-4748-b937-5efb6fefecfc" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5355_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-004149-1026_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e331b564-d79c-446d-bff2-a732dacba6bb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "f73d9c17-c497-5025-84d8-e9adaf48a245" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-MT-A67G_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "63535469-d402-4ba2-9ab5-986e6ed80f55" ; + crdch:id "7206e2ea-ad1d-45d4-ba3c-fc1f39fc52ea" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -20834,89 +20281,122 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "256d61e1-54c4-4250-bd17-5bb82496f5f4" ; + crdch:id "25588932-d586-4a17-b18e-4ede4292ce9e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c2ef7833-c2fa-446c-a12e-f353c744b1e4" ; + crdch:id "6b690841-3ad9-4919-8913-8f291ee95868" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "155ca101-ad45-4f50-b9ac-45908daffab8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0003009-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f8de95dc-1011-4b86-9a46-28bc46465195" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3cd3b53e-38ff-454f-8b3a-d7942696429f" ; + crdch:id "192c4be7-66ba-416a-abfb-1a88e63e7be4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015915-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-VICC-534918-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:05:42.341898-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f48ed568-6c4b-4746-b480-139ed3ab5794" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "e15f8344-5f7f-4602-b2e3-8fcb0418cb8b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -20924,26 +20404,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "fc0ee2ab-b738-49c2-b645-4b6851be5e8b" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "523155c1-e181-4d6f-9873-9449a8e3c289" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-49d6a6ea-metastasis-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-036955-74886_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c63e4630-7bb4-4f01-b9fe-94478000158a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "9ed6f000-4643-4f65-be84-8fd380d3bc36" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -20954,23 +20434,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1137ba9a-12d3-4b2d-a3a4-d95de8bcf49a" ; + crdch:id "e769c390-13f6-4054-8182-017360bcfdca" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-8191e4ea-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-004469-15_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "783e6c97-20aa-4c8b-a7e1-ae0d8f7af28d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "ee78495d-54c1-4d73-93d7-06034b0c7bd0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -20981,72 +20461,39 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "64881717-bcb2-532a-b0af-395ba5c62c2e" ; + crdch:id "be57683f-0245-4929-89d2-98740dc99b8c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6481_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "GENIE-DFCI-011271-11674_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "04652163-a674-446f-9e86-607de19e4c34" ; + crdch:id "fe032782-a750-46b3-a282-26e110ed063a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e9a39a90-6401-4a9f-baa5-606e8b5176f6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; - crdch:system "GDC" ] ; - crdch:text "N2a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "7a67eecc-6f46-5181-8b64-c022d0fd0060" ; + crdch:id "20846d6c-1a34-5e01-a531-f9c783416c3e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BB-A5HY_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-MZ-A6I9_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; @@ -21054,42 +20501,48 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4467ee1a-7188-49d6-a0d1-c8e395e6cabb" ; + crdch:id "0551272d-7e05-435c-92b3-918cde4d14ee" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5c2b4403-cdd4-4550-ba01-d8ebad9fcbc8" ; + crdch:id "396f116a-bede-472e-847d-435a77dfa7dc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "589cdde1-ecd5-4a7b-9cbc-3186916822ab" ; + crdch:id "f32ce523-c60e-4a86-bfa0-eeb4f3b2d83a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], @@ -21098,147 +20551,55 @@ crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c239680c-7353-50f5-a155-33973562e904" ; + crdch:id "203f4d20-b796-4745-9bc0-6385c28ff0ba" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A45W_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0003320-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fe66156a-b3ea-4ed1-a5ca-68a3664c3505" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f9ae08e7-9166-4699-801a-4bed11f72dc2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7202ca4b-6caf-4f4d-adc9-4c59b00cbdc3" ; + crdch:id "3a006479-c2eb-457a-b0a1-e3faebae25b9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f87fc232-ea15-4a26-a863-8604cdb8bb06" ; + crdch:id "3cd3b53e-38ff-454f-8b3a-d7942696429f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037287-88492_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0015915-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "421f819b-c4ac-445f-882d-c36766f7002a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "f48ed568-6c4b-4746-b480-139ed3ab5794" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -21249,23 +20610,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "740bf7b0-dfdd-4930-9cc7-3790cb8808c1" ; + crdch:id "26a2438a-f914-4865-9784-a9a47150cb4e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0005212-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-010260-9348_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6e2561a0-676c-4f69-9059-d49696a56c64" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "0d696183-2cc4-4f33-9973-04537cb86276" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -21276,104 +20637,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "8f722b2d-eb3e-5b8b-8b36-429137cb0a3f" ; + crdch:id "9808f3d0-16f0-519d-8e0a-9061968bc749" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7383_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CN-6023_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "887261fe-5b99-4722-aca7-4e63a0b63336" ; + crdch:id "ae1a6096-8d51-482a-8c44-cbfdc7dd6458" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6237b644-9903-4f45-8b07-6c610b1342b8" ; + crdch:id "5e42be68-8865-4c69-8684-0f6e5c6c9b94" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "0bc27973-621c-4011-bcbd-3b7f3464389e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "11f5b868-a6eb-4575-b5d4-54cd8a406293" ; + crdch:id "9d41e68e-c648-42ea-9320-6e08b9b5dd4c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-027923-87624_diagnosis" ] ; + crdch:value "GENIE-DFCI-007598-4084_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4e763f63-0494-4b2f-9f6a-c9461c7e7b1e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "87d18b2c-1241-43b3-b7aa-24442a047ade" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -21384,131 +20753,106 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "396ba806-81a2-43e2-be95-276cdeee09e3" ; + crdch:id "e61558f0-d90a-5bd0-8485-ba159dba3010" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0003049-T01-IM5_diagnosis" ] ; + crdch:value "TCGA-BB-7862_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "162d69ba-adac-4884-9d98-3bc70cdb72a7" ; + crdch:id "091478b2-f8c5-4ad8-9c89-06a48728fa2d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "22e091bf-8af8-5910-9664-c73e7b5f44fb" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-6487_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "027dedd3-bd53-420e-b7f2-eb5b8c26bcdc" ; + crdch:id "fbf59d12-7047-49b1-9002-00030c797438" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ff63290d-0644-4387-99bb-697150a7fb6b" ; + crdch:id "a61be572-405b-4b16-b554-7fa6c12a48a4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; - crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6b76278a-cb58-4308-bfef-fa1902a02375" ; + crdch:id "d0fdd332-a86e-4d6e-b93f-97937926a834" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010467-10870_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0019630-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:43:52.092583-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "02cf8f79-3109-423e-b290-9b0cf112e827" ; + crdch:id "bbc31a15-3dc6-479c-bd5a-9c1950705ca4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -21519,139 +20863,109 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "78608de5-dd5b-43da-8934-e0b6fa924ab4" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-4493-11651_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "8955be34-dfc4-4a5e-9636-f27ccef4318a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "35b1cfb8-bac8-5abb-85dc-1761cd25e90c" ; + crdch:id "a37311af-d40e-5c8f-ba14-b3b2ae22e486" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A5Q6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CN-6997_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "8b73f661-e1ec-4bcb-9eea-a5e66237229a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1ac65133-fc2b-4b41-a101-eacd225f71b1" ; + crdch:id "00a721c6-6cb7-4408-a63a-6dae9310a3fe" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "73005780-ea15-4353-b6f7-c26865d3f4d0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b929bf9b-34a0-4fa3-9bd5-49f8097c573e" ; + crdch:id "b4c9a3aa-151e-478b-bc18-ce793b68ae09" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N2c" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; + crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; - crdch:system "GDC" ] ; - crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "N2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c1111640-7729-436a-9b46-88c0ab534b96" ; + crdch:id "7bfa067f-69be-4a58-a8a7-98963ee8c589" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-832679ee-sample-a_diagnosis" ] ; + crdch:value "GENIE-VICC-493620-unk-1_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9590434b-5b17-4ee8-b109-7ebb737252ef" ; + crdch:id "57a1d12e-9ead-43ed-8990-0fecb573d3cf" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -21662,122 +20976,153 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "0e8b9b8f-041a-4d83-8af0-503b7d84e00a" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "47de90b5-a5ed-5ce0-ada8-7f2c8e621913" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD4383_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-CN-A641_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:07:26.436903-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ea5776ba-c4cc-4d4b-9e33-573ea824853a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "cc3866fe-2690-4354-a548-10189054b85d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "96053970-fb5c-4b79-b1bd-8eb8690def1c" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD1118_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:text "Not Reported" ] ; + crdch:id "0c14d932-3b44-48fa-8974-db6e01464851" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:12.328231-05:00"^^ ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8f636ed2-41a2-4c3d-bee5-40d9755bf674" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "744cbf84-554d-4cba-aa4f-4c1e5e28a1ee" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2edff908-b791-5c44-b0ed-cdbad3c1a249" ; + crdch:id "e3d5bf4e-2856-5604-a086-3e4464a68c05" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7418_diagnosis" ] ; + crdch:value "TCGA-UF-A7JF_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "26eac019-6e9b-4ab1-aa1b-323f76d9aef3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2e5b2590-4227-4265-a837-8175920e4d01" ; + crdch:id "f4cf2a66-8872-41ee-8270-296d5f76265f" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cc37f4d1-d8ae-4367-8abf-7c6da579d09e" ; + crdch:id "7ce8968e-f693-4fa2-945a-0cea27c96ede" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ccd7a7be-3065-4f30-8d21-94bfdc0b4703" ; + crdch:id "f4e12699-7e71-42ba-994a-c3a9a71a95cb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; @@ -21790,48 +21135,78 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T4a" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "8c624d17-a588-40ee-9902-ed694d794814" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "AD1281_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:system "GDC" ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:02:30.028866-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a1fe6dde-024f-4487-8838-24fda3505cc3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "64ba1bbd-bf72-4700-97be-0bc054876c84" ; + crdch:id "cac9736c-3015-486b-b69a-906d2bcbac13" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005062-1372_diagnosis" ] ; + crdch:value "GENIE-GRCC-a20580bb-sample-a_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a0deb101-019f-46d7-8cb2-ee98c9d7aa92" ; + crdch:id "cf3feb17-3b74-4d84-8395-c4af9b8f4514" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -21842,23 +21217,23 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "c9269eb1-ab75-4719-8cd9-e9efd32f7d7e" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6c55b480-1444-4ae1-a079-72287e8794a4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-5245-16353_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0017687-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:07:22.808668-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:37:32.909734-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "08209047-3b7a-4295-90b0-ddc92aa1e1c9" ; + crdch:id "52f200af-cd9b-4d63-91fc-7bf44c67c537" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -21869,372 +21244,403 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "3ddf3ff8-b8b0-5525-8425-dbe1c27753b6" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "6284d2ec-e8b6-5cce-957d-f55704379de9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-IQ-A61I_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-TN-A7HJ_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; + crdch:text "8071/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "19c823d3-c15b-4a1c-9a27-6ce489f3b640" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "cdc66ca4-8864-4f22-bc4e-8fb5e073937f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "68604eed-fd8f-4003-b9bf-ad0e1ecdf3b3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "412fe306-9755-4efe-abb0-9af695b5691e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f238d98a-1b53-4aae-8bdf-f85f0b9a066c" ; + crdch:id "50df1144-990e-4357-8a15-132289bce0d8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "NX" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "5606079e-0d29-5f59-acc3-d6de7b479a24" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CV-A461_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "76af13f8-fcb3-4324-b8aa-23ea1834c5d2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "af7bb799-b091-45d9-a04e-074bb7840680" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ac4430c7-dbe4-432f-9763-81707431a0f0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Stage III" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "a4332fc7-aee9-497b-99ba-5c1d548a7623" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-037277-88571_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d2ad484e-58b3-4e29-84e3-a45abb294b3a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "d078cccf-6335-4c55-8d5e-a36e32dd8006" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-004034-372_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "7d1a8a2e-c9d3-4e1d-b183-3c82de7e2306" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0584ee86-f589-5812-9bad-03855a31693b" ; + crdch:id "6ce57628-3cd7-5cfd-8317-cadf76a37f43" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-4076_diagnosis" ] ; + crdch:value "TCGA-BB-7870_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5fe1ae56-74a5-44a9-b8d1-7f05a569bb34" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "0d53784e-011f-4890-9cf5-59e955dd1fea" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fd99fd83-4040-4738-8a5a-e42d36ecfe0e" ; + crdch:id "b79164b1-7abb-4585-b23a-0e610734ea8b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d6f48bb2-379a-448d-b13d-2dfc5da91d0c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "f5589c89-0b94-4492-8a3c-84d58377e94f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ] ] . + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "066a4a47-3b4a-582d-984d-476fa8a4fc57" ; + crdch:id "5a687c66-0c8c-5e23-bd7c-6988abb14d66" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7422_diagnosis" ] ; + crdch:value "TCGA-CN-6021_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9e25f49c-cd83-4171-9e07-51aca3fb1019" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "edcbcb1d-23bb-4177-8f77-71071822cd89" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "63bdeeca-a7b1-47fb-9945-c24f7513c56c" ; + crdch:id "f1cbf326-7657-4c9b-9c8d-e2036e89fd07" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2c2db97c-8c8d-4f1e-ab73-469238609d61" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "619a1a7c-f360-4e07-aa85-812e2b1bd92f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "f773f13c-c661-46fd-8bd1-56dae4502465" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-8057-18231_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2af6ce71-3d6c-4da8-8b75-f0ae49f95bd2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; - crdch:system "GDC" ] ; - crdch:text "Malignant rhabdoid tumor" ] ; - crdch:id "d813126a-5e28-5c5a-8730-598f0d047584" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TARGET-52-PATBLF_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; - crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; - crdch:system "GDC" ] ; - crdch:text "8963/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "ac3e795d-69a1-57f5-9dec-5b59e2523091" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; - crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "eb5eeeae-6bd7-511e-9f13-51531684c774" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; - crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; - crdch:system "GDC" ] ; - crdch:text "unknown" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c58ca3ba-23a8-472b-aab3-94382be12940" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010867-8727_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "d492bfd2-b37d-49c3-a8d5-40171e8442d5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "T3" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4bcd5e25-adf6-5fe2-b07f-05d72b7b22a1" ; + crdch:id "f41a7343-e52e-5f4b-b902-ccd3275b00b9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A6T6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:value "TCGA-DQ-7589_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Gum" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6f0b02c4-6efb-4104-89e1-2e76811b6afc" ; + crdch:id "19c44a45-4f80-4d5a-beac-83db256a3434" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e22036a1-ed2f-44b4-8bca-bd9808611fd0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -22242,89 +21648,73 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3147ba3d-b1fd-4e40-82e1-56429f2389d6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "127b2222-93b1-4870-93f2-867d8e69d015" ; + crdch:id "41ec6e82-6bcd-4057-a370-bfe1801e2e94" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; - crdch:system "GDC" ] ; - crdch:text "T4" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage IVC" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "M1" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "0ea10d4e-1809-4763-b440-8e077ecab3e5" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "130676ad-54bc-4d20-9ec5-129d4688296d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD17629_diagnosis" ] ; + crdch:value "AD1478_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:55:27.721574-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:54:59.697804-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9ab974e3-bc94-4f83-b7dc-82285f5b4b69" ; + crdch:id "50977953-c3a2-4b71-b40a-3f211a269cc5" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -22341,139 +21731,184 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "81d9c62a-5f07-4409-aad8-4f9e02b90669" ; + crdch:id "d284c064-ed2c-5741-b1ad-2f9fd34b6636" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0015745-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-BA-5153_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cd31b18a-5019-4a94-8966-a1160e544684" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "2f668e36-b359-488e-b0fc-fb7bb479f485" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "2dc7070a-9c70-4bb1-9634-8c934bb9c8d1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f079e825-160a-40d5-97cc-1931f11c4e2e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "91287016-0fd4-5434-a010-e392bd679282" ; + crdch:id "59b73fbd-93ab-5cbb-b052-82d5e66a4c16" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A45Y_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-5249_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "01a4aa4a-f073-435c-a411-839760cbcb9f" ; + crdch:id "6697dd71-5a58-4862-b26e-ea16dcc383f2" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bbcc5141-d805-457d-bc4a-d424c8c39cb7" ; + crdch:id "b72390d2-f19e-493d-9a30-cd81dd232188" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "26026e2f-b112-4535-97ac-6956cb267e9e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "85d63c6e-a6c1-47a5-92a9-216719073a4a" ; + crdch:id "56566536-d3a4-4103-bd5b-550ceaad2a6b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004072-413_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD5017_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:53.493092-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9a26d9df-9ab2-48df-ada8-8bd8455cccd6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "e2edc535-6fc4-4999-aa4c-932bf58d344e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -22484,116 +21919,113 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a71bc3c7-5807-5766-8487-c3dbc27484cb" ; + crdch:id "40954a8e-e4c2-5604-937b-0a79ac7489d2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-5243_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CV-7261_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d89d46ea-9a7a-4fd8-b11e-9c9ca4780119" ; + crdch:id "69a89590-eb61-41d5-b33e-e7bc5adb92bf" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b069c55b-496a-4a57-a507-1b2e1b4201ae" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "00f7bc3c-c0e7-42bf-84d7-87a8a539bd4a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6fc08372-0d9d-4b3c-b656-9573fa532c99" ; + crdch:id "a7692585-a129-4671-bfe5-98342a326776" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ] ] . + crdch:text "Stage III" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "366df7ed-b836-4cb0-9146-75d22e0ca019" ; + crdch:id "430602f6-cd8b-48d1-b519-dee691fc9c20" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009836-7821_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0003106-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "356353d1-c8db-4f97-b1d2-0b895cb42266" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "99aab93f-633d-4ce6-8ccf-36cb05c5d2cc" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0007575-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b1d7b582-2302-44fb-a98f-13372ca17247" ; + crdch:id "78b77808-ec88-4e6b-8393-decaa7bba86d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -22607,23 +22039,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c4b50b5a-dee5-481b-8c34-5584abba267f" ; + crdch:id "6d395db6-3f58-4c4a-82dd-9b3b9c35fc8f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-UHN-614933-ARC1_diagnosis" ] ; + crdch:value "GENIE-DFCI-004670-873_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "09f9d0e6-10af-4224-a875-8d1e99e90eb5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "3396e2a0-10bb-43b3-b5be-7980064889e0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -22631,66 +22063,104 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "dabe6d0e-8f19-43d7-9e3d-02a6a24556c8" ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "3ddf3ff8-b8b0-5525-8425-dbe1c27753b6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002411-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-IQ-A61I_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "68604eed-fd8f-4003-b9bf-ad0e1ecdf3b3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e1e98bc8-81b8-45f0-8289-6c306defeaef" ; + crdch:id "f238d98a-1b53-4aae-8bdf-f85f0b9a066c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d55686fe-0423-4b01-9719-ade00bed3004" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0009761-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "64dd4e81-f01b-4846-b306-20b7cd7d9340" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "19c823d3-c15b-4a1c-9a27-6ce489f3b640" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b1c3bd39-9f13-5dba-aeeb-86271bf64b8d" ; + crdch:id "c0bf8ccd-6f3b-5ede-b3ce-a63ad584ab1b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-7242_diagnosis" ] ; + crdch:value "TCGA-DQ-7595_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -22700,14 +22170,7 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a45efd70-9bee-4c18-82b1-666d2c1eb781" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; - crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "4fdddf85-30de-4666-89d2-0683e9264d6d" ; + crdch:id "c522234a-c0b1-427a-8992-84fcfc9389ef" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -22715,21 +22178,33 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6b4b146e-e6c5-454d-9c4f-66a6f851c3fe" ; + crdch:id "52e0aaf1-d93b-42f8-b0e3-f6b4a3d0bd1e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f9dea7a5-e9d2-48a6-bbc1-c5c1f8e7ee67" ; + crdch:id "387e8df2-f053-4cbe-aae8-5727d215f904" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; @@ -22738,245 +22213,134 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; + crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ] ] . + crdch:text "Stage II" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0cf011bf-054a-4eea-aacc-b963ff83734a" ; + crdch:id "126d74e6-2981-5aea-80e7-62ec5cff609a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007960-5976_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-4739_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c353a3fb-dad8-4a6c-acd3-4121eb21b98e" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6b3df15b-f5c6-4c79-923c-572688a90a50" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD1220_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:id "b916fa4a-1d15-4619-9d6c-1000e96b7e0d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:57:01.408534-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2bbdf4c4-88a1-4358-a88a-5daa2a9a506d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "18d11972-ed5f-4c5b-9511-18b00bca7f7d" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MDA-8036-18260_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:id "f450dbe6-4972-4c49-af97-963bcd0d0da0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "475098e0-9927-42fc-adf2-e280d8aec3bb" ; + crdch:id "9491d6f0-1e3e-48e5-aabb-87704511904b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2602d676-8c2e-5bdd-9790-a0a072d3f670" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-DQ-7596_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "61c82e56-e64e-4fcb-bc5f-dc4fe34b6c58" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "7a94106d-5604-4b73-9c54-54a72b12f52d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f662e970-6a51-4164-8458-61e7ff054806" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "e71fe2d8-2dc3-45b4-bc48-25b118a6f909" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD2206_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:54:31.122378-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "68742842-28e9-49db-b49d-79c73ad4ef0c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cac9736c-3015-486b-b69a-906d2bcbac13" ; + crdch:id "1ebf1ce6-31bd-4c8e-b3e0-f70d47cdc527" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-a20580bb-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-MSK-P-0016351-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cf3feb17-3b74-4d84-8395-c4af9b8f4514" ; + crdch:id "90f2519b-17ba-40ad-baee-cb711b306a91" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -22990,94 +22354,49 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "51ca5228-56c7-5d68-9285-1bbfbe8b4492" ; + crdch:id "309da786-ca2c-4c3a-8907-5e690f375f54" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7370_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0008800-T02-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "0e357973-d52d-4fc7-8099-7b87458745e2" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "339524bc-bc1f-403c-a12f-6e8ce72fba50" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "5dec4e0d-afbd-4ad6-8acc-00b5ad113a03" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; - crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ] ] . + crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Adenocarcinoma, NOS" ] ; - crdch:id "5d2d67d1-4611-4a18-9a66-89823aaa8e3c" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "07feaa02-95ec-48b9-83ff-ddd765c8ca9d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD6426_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0006098-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8140/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:44:57.790971-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:02:01.981535-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bdc73f48-dc0b-487d-abbe-e3a977b6830a" ; + crdch:id "eca4b442-f9d1-4018-94cb-158757bd3bea" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -23086,26 +22405,29 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5fddab5d-aebe-4b6a-9812-a6edc05c51cc" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "1fdf9d03-4341-4aaa-b47a-98f1221816ea" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008897-6910_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD3249_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:00:26.233095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f8a73605-d802-4364-aa6e-5d23691f92cf" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "425f42d0-0349-42bb-9072-cfb0bd97e922" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -23116,20 +22438,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f0b5d732-2466-4d9a-90cb-ec3084606849" ; + crdch:id "ad265c45-3ba4-4f8a-afcd-70d7f2e79751" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010677-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-DFCI-009344-6546_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T19:11:18.668081-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e084b5e5-05ac-4229-bbe8-f640f231e1fb" ; + crdch:id "b993e287-e823-4843-b182-3bf775dfb489" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -23140,25 +22462,28 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "274578bf-55cd-4807-9c8e-573db026da1d" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "4f1912bc-3704-49b0-b916-6d0e99463553" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002592-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "AD5075_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:07:48.972608-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a75ac689-6228-4806-b699-874f8ec28ae1" ; + crdch:id "dbf24e2a-1a10-4dfb-be35-8021f82b947c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -23170,23 +22495,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6cba02c0-48e0-4424-964c-a104a6652d07" ; + crdch:id "5a82f834-a2f8-4d61-a816-c410213556b4" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007903-6035_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0000319-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fbd21489-29cd-4d9b-8d7c-e04342040edc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "d0ef535c-d0ed-471d-a1a6-3cf9600d37cb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -23197,50 +22522,91 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "915d0d2e-63da-4723-909a-4bece5afab90" ; + crdch:id "c9ea5a2b-8b14-5745-b9c3-c93c9abe468f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0018175-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-A45O_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Gum" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:39:49.045696-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "fce64b88-8be6-4710-83be-18c9afdf13ed" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "ec7fe5e6-74af-4bd2-9ecb-8e302f763b22" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "d4ba57ac-0820-4d57-85a6-06122bb4559e" ; + crdch:id "77b774a4-9456-4907-86e6-9ff2dd87b8fd" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e87ea1cc-7728-4592-9eeb-04d09e11660b" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "08272717-6b2b-4734-9674-4bec2662bd32" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0005082-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-UHN-523097-ARC1_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:18:10.730001-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f9e5d21f-2ee2-41c2-b864-f43d6a8357aa" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "ffef8dac-d99c-4426-ad9e-f4e3947fe1c1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -23251,95 +22617,130 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3f9d8932-dc6a-4225-b085-953225ae22ad" ; + crdch:id "48994484-82cc-51ba-a8b6-6f4663599d40" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0007407-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-6478_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "dfbc5ddf-a361-4d72-ba8d-5615ca644357" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cd1a65bd-7bc3-4c1e-9d5e-792938c2fc5a" ; + crdch:id "a26d04d0-1501-4cc7-afea-154a89cff0ff" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "f7044868-4f81-56df-87a1-58bd49f9c8cd" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "cdd012e7-6539-5ffe-a4b7-b36a6233b1ec" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-A6V7_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-BA-A6DJ_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:text "Gum" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "69fe86c3-1e82-4583-9051-ffdb84224239" ; + crdch:id "735334b4-6c30-4a7a-aa54-63f506b8e2bb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ed5933bf-adaf-4bee-81fb-b1ec5782c248" ; + crdch:id "bbee89dc-6858-45c3-a9fc-c455851f96a8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "4210ffee-2a83-4f05-8935-2687503c83d4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -23349,22 +22750,28 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2dd60fd1-68e1-519b-af66-00c32d0cb6d4" ; + crdch:id "8723983c-94ff-55df-8165-6fd5937b5462" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A8ZB_diagnosis" ] ; + crdch:value "TCGA-CN-A63T_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -23375,215 +22782,315 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "44c64654-0e37-4c13-b4fa-aaf9c6644445" ; + crdch:id "75c0a7b6-3e82-4ce9-8856-dd3475affe87" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "17a0a479-3b48-4852-ab06-dd33d6f7788a" ; + crdch:id "b477dfb8-c039-49d5-9a0e-912946dc3ad1" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "936a8a93-6559-4bf8-9c51-e81ec4f2aff7" ; + crdch:id "74606f8c-46a7-453e-acfd-91203aec6df7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "fb2076bc-c2ef-4566-ab26-c6c6fcd212ed" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-GRCC-b3db0c02-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "01b01d59-07d3-481d-b466-bf77a916a0db" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "6dd63ec3-e88a-4da9-be07-0d11a1768dbf" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0004416-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "34487c7a-5f9a-41b0-8ced-d7c2ce3653e2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; + crdch:system "GDC" ] ; + crdch:text "Basaloid squamous cell carcinoma" ] ; + crdch:id "fb148e0b-2d1c-57ff-acd6-4f2208af3ce3" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-BA-A4IH_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:system "GDC" ] ; + crdch:text "8083/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "eff60f0d-e3c1-4a93-9026-c0764c70ba9f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f87efb5e-24f5-4d2b-b6b3-987bbda30e03" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "310c112e-7e2f-4987-a515-fe213ae70986" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002198-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b9d46cb7-1679-4998-853f-03e5827cbb53" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "86e71958-485e-53c6-831a-c456ec617b7b" ; + crdch:id "d852d062-d7e0-559b-8492-da2b0abe8415" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-HD-7229_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-6470_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f1367475-a5f1-4a0f-aa73-5a703a3accaf" ; + crdch:id "afb7ea63-2959-4e53-95ea-7a032dcb5a8b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9fbf3123-c654-4f2c-b41a-ac4dc029a5d9" ; + crdch:id "aa121605-a2c9-43fc-a836-8ec6c42b99de" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "1169973a-8575-4d2b-8da8-36a83aa5f947" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "stage ii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "Stage IVA" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "aa6e25a1-2d85-423b-a149-8cf11a6947f7" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "8d28ba70-052a-42c0-9a4e-f06ea143f381" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-010697-8404_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-MSK-P-0001195-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "22ef8279-1519-4099-ae13-ff430645c992" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b857d450-dfaf-4407-84e8-d3bbf843cbc3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -23594,109 +23101,112 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "24058118-f7b3-53d4-b24b-07a2ac2e66b1" ; + crdch:id "a8a92864-8cd0-5e1b-8451-ca6f3e84a857" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-5369_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; + crdch:value "TCGA-QK-A6V9_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Palate" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8d31f35c-9178-447d-9a2b-acc305fab407" ; + crdch:id "30ad1a00-b48a-47bb-8cfa-d65e4c4ba125" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b4c02606-0f86-46e4-9daf-dc7dbcd60d78" ; + crdch:id "462748e0-b611-44d3-b3fd-efb762ba317b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "11d697ec-f451-4102-a908-e44f48ab0800" ; + crdch:id "9b60705b-95c4-4079-a907-e4a4b65a3cf4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "Stage II" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "stage ii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e769c390-13f6-4054-8182-017360bcfdca" ; + crdch:id "65bd5ce4-bf44-4994-824e-f21701449f73" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004469-15_diagnosis" ] ; + crdch:value "GENIE-NKI-HMII-Q9EY_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T17:51:39.178920-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ee78495d-54c1-4d73-93d7-06034b0c7bd0" ; + crdch:id "cb629447-dbb7-49c7-a88a-435b6b6decda" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -23707,28 +23217,25 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "533bd04a-5e63-4ae1-a929-487ae3597956" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "49e46e5d-46b8-41f2-954e-c3c7b563a55b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5852_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-041937-203493_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:25.573239-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:28:08.827884-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f7b249aa-b35a-4e08-87b6-e9a79d75edbd" ; + crdch:id "1108ef37-87b6-4b62-82f3-5e799fc4fb52" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -23740,20 +23247,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cae73de1-65ae-48fb-a08c-355e6921dca5" ; + crdch:id "c96ca96a-8046-4381-a767-1119705c5500" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006462-4354_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-DFCI-008037-6376_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:27:14.117499-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:11:14.458475-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f632701a-5242-4839-b96d-0214c7e9a73e" ; + crdch:id "f5e6b025-48ca-4fd5-b657-ae622bc9de02" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -23767,20 +23274,47 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0bf30179-24b0-4b0e-856d-7226a72eb3e0" ; + crdch:id "3cb5d51d-2566-4b1f-ad4f-57520007e73d" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-052973-173599_diagnosis" ] ; + crdch:value "GENIE-DFCI-050743-203353_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:20:30.865187-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:18:25.269226-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b39fb248-8053-47b7-aa2c-d69335f218ce" ; + crdch:id "c862481b-aaaf-41d4-9c29-188760a43dd8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "dabe6d0e-8f19-43d7-9e3d-02a6a24556c8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0002411-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e1e98bc8-81b8-45f0-8289-6c306defeaef" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -23794,20 +23328,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "23193585-2a17-41cb-b577-8044058658ea" ; + crdch:id "9e0b865b-296f-481f-8bc2-7bfe4642d805" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-8k5ygy35-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "GENIE-MSK-P-0001912-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5db1c5e8-ddbb-4057-a059-6acf46826258" ; + crdch:id "271c4064-6b2e-4971-853f-e3f2a1cdd74a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -23821,9 +23355,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c97d4793-3b4b-521d-a274-2d1dfeda79ae" ; + crdch:id "18a6869d-fcbd-526c-a71f-7f5145b12278" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CR-7398_diagnosis" ] ; + crdch:value "TCGA-CV-7440_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -23833,113 +23367,182 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "251e8544-2c3c-4b31-a2b4-29b57e6ee4fd" ; + crdch:id "80eca6e9-b390-4878-a070-e40c1c19b1f4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "bb0c2fd4-8ffd-4825-aaf2-e865090940c8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "13348e4e-8b8e-44b5-83e6-a1159a53ea35" ; + crdch:id "86b81c8d-ae15-477a-86fa-6e10f1263f87" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "1d594963-b5c3-496e-af52-5f6dbcd6910f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "NX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "Stage II" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "60d7b883-bf64-4777-9f6a-efaf4c4a40c4" ; + crdch:id "8f722b2d-eb3e-5b8b-8b36-429137cb0a3f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003875-1298_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-7383_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c930148f-2059-480b-960a-4efcb3c98ac1" ; + crdch:id "887261fe-5b99-4722-aca7-4e63a0b63336" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "6237b644-9903-4f45-8b07-6c610b1342b8" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage i" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:system "GDC" ] ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "972c3046-1f6c-40fc-a83a-3b200148a683" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "da37f4a4-3f09-4771-a1a0-9b2ce6e0df03" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5830_diagnosis" ] ; + crdch:value "AD2161_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:39:05.012118-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:54:06.130101-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ed2a5846-de67-40c3-9074-3adc9edfb0b0" ; + crdch:id "7f5f0ba4-3eb5-462a-8db8-31faca9d0d27" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -23953,83 +23556,110 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d0fdd332-a86e-4d6e-b93f-97937926a834" ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "43cceeb5-008a-58cb-b219-34c3ac43e86f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0019630-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-A497_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:43:52.092583-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "bbc31a15-3dc6-479c-bd5a-9c1950705ca4" ; + crdch:id "882c6ec3-1f56-43c3-8a41-da060f9f5ee1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "bea32bd5-4068-4351-994e-09b3bf819ebb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "fcd7326c-3bf2-425a-b117-f1e5f6910db9" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-c9c06784-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "43bdb66c-6b5a-4a1c-9d44-2717ecc981ed" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "426ed511-e284-4ddd-9809-312805a88905" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "5ddc8873-1487-4787-8a1d-3b116a2db42a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD3816_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0010816-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:01:59.757092-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3fa16cbf-829f-4097-ac9f-d8016c40c618" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "e179e193-0933-48cd-98fe-aa4e21c0ad44" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24040,19 +23670,26 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5606079e-0d29-5f59-acc3-d6de7b479a24" ; + crdch:id "1ddea2fe-7874-5d31-b1fe-2cb2b0de542f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-A461_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-KU-A6H7_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ac4430c7-dbe4-432f-9763-81707431a0f0" ; + crdch:id "840d3da5-0493-460a-b5a9-4285e1a2ad37" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "b4074f91-5478-4117-bee5-ed164e4d38c2" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -24060,68 +23697,95 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "76af13f8-fcb3-4324-b8aa-23ea1834c5d2" ; + crdch:id "61eec5b6-925d-434b-a318-b22fc21c9ffe" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "af7bb799-b091-45d9-a04e-074bb7840680" ; + crdch:id "e4439379-d930-4b9a-b498-3b75e569f8ad" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "M0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "ca8f5806-a2af-45ee-8217-e6dfc4d0b229" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "d7acd35e-0ca1-42f0-932c-a3cdd6f8d09b" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0012391-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-037833-36073_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:17:29.664139-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3c8fe733-1711-4d4a-a64c-b94788eda279" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "8f775235-6026-40f6-b156-cc3711222412" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24132,9 +23796,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b588dad7-169a-5ecf-885b-580be11d01cb" ; + crdch:id "556216dd-a648-5f7e-a4b1-8f8688a354b6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6992_diagnosis" ] ; + crdch:value "TCGA-BB-4217_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -24145,60 +23809,60 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b86352a7-2987-4743-aa3c-1895c438641a" ; + crdch:id "3d9307b9-f42f-421b-bebe-ed692a5868ce" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7a5921a4-5714-44e7-8ebd-048031b32b88" ; + crdch:id "5eacbcc3-8ac1-42bc-b3dd-53bc693d3cae" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ce0b9c55-baeb-4ca8-9235-51a836a4b58f" ; + crdch:id "b9427fad-04aa-4e73-99ba-ccde04e4978b" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], @@ -24208,57 +23872,36 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b5616ad7-8322-44c9-8b64-01314decc5a5" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-GRCC-9df16b49-sample-a_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "3dc819bf-5af3-4be1-a892-974d670975c9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Stage IVA" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e7406302-5dd6-45b1-ae98-a8094c495943" ; + crdch:text "Adenocarcinoma, NOS" ] ; + crdch:id "5d2d67d1-4611-4a18-9a66-89823aaa8e3c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD13780_diagnosis" ] ; + crdch:value "AD6426_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:40:26.338588-05:00"^^ ] ] ; + crdch:text "8140/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:44:57.790971-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c9bccdb4-1bd0-44e0-bfb0-7588611ab01b" ; + crdch:id "bdc73f48-dc0b-487d-abbe-e3a977b6830a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -24275,20 +23918,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "cf973339-e31d-4fb3-833e-f954634d95ee" ; + crdch:id "a433a5fa-fd34-4ab5-a117-29614a2c7f9a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0014965-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MSK-P-0013513-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:42:39.927651-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:39:05.576558-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1bd46cb2-e563-4a48-a36e-ea4f7a15173f" ; + crdch:id "f2ec974c-b952-4450-947b-11c39bbaf248" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -24299,29 +23942,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "da37f4a4-3f09-4771-a1a0-9b2ce6e0df03" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "d8e6b6ed-5c11-4a78-b25a-07f23305bb40" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD2161_diagnosis" ] ; + crdch:value "GENIE-MDA-6285-17334_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:54:06.130101-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7f5f0ba4-3eb5-462a-8db8-31faca9d0d27" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "8479ff0a-fce8-4f4e-8d00-6775d1e9cb00" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24329,26 +23969,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "2ba98ec4-5cc5-43d5-8de3-ab33d0d6779b" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "f773f13c-c661-46fd-8bd1-56dae4502465" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003996-1286_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-MDA-8057-18231_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T19:10:26.105156-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "12d6861e-5ad9-48f7-ae61-07c7e45be5a3" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "2af6ce71-3d6c-4da8-8b75-f0ae49f95bd2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24359,171 +23999,91 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4fdd25bc-4056-47f1-8eb9-7e572313ba5d" ; + crdch:id "c8d65c8c-9299-49bc-bfe0-97c19ff35fd2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009927-9027_diagnosis" ] ; + crdch:value "GENIE-DFCI-037050-88705_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c65b0cad-f2f5-40f2-a523-60374faf390a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "8764fb2b-e701-53db-b137-03efa2c52637" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A6DI_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; - crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "e7a7e296-3f1b-49f5-bbaa-082f918d080d" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b0d4b16c-cc81-405f-83a1-de57cb488166" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7b56068d-21e9-4879-b747-c99943e40e50" ; + crdch:id "58a5858d-4740-4da1-8959-43d7b05ae1ea" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; - crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; - crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; - crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "424f3fdd-09f1-57a2-99de-10c13b9be653" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "cecde3bd-c011-5cd9-8071-912a0f342eb8" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-A6EP_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:value "TCGA-UF-A7JJ_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Hypopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1e8ad4ff-09db-44f6-9527-b10ac22453d6" ; + crdch:id "de8517e0-d7ad-41a2-9468-bdf0106c905c" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "661cafd9-0cf9-4c6f-b541-293bdecf3ede" ; + crdch:id "408c2c68-2f92-421e-b797-ecada0bfedc7" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "434adba3-549a-45f7-b89b-76737678ae0e" ; + crdch:id "392cbac9-ed5a-4f0c-9270-f45278476c73" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iii" ] ], + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; @@ -24536,37 +24096,58 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "T4a" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "1ad86ae6-e1df-4578-9639-e768e6711e61" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0008033-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "28cb9e1d-c34b-4909-a387-5a5c60bcd6e3" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T3" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "671671bc-dbf4-4e15-b978-6aceaac1533f" ; + crdch:id "0b96cae3-d332-4e5e-ba59-e0a6bc6573df" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0016761-T01-IM6_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0017105-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -24577,7 +24158,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "0d989563-7a49-49e9-9417-4b607d661ab4" ; + crdch:id "ba279369-073d-4976-8439-3a318c0f0fc3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; @@ -24591,109 +24172,134 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a08be31b-24b0-5fb3-b49d-955fcce7603c" ; + crdch:id "366df7ed-b836-4cb0-9146-75d22e0ca019" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-6827_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "GENIE-DFCI-009836-7821_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2ef80e58-961d-45d6-ac3a-a520be3728c9" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "356353d1-c8db-4f97-b1d2-0b895cb42266" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "f7044868-4f81-56df-87a1-58bd49f9c8cd" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CN-A6V7_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:system "GDC" ] ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; + crdch:system "GDC" ] ; + crdch:text "8072/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "460e7821-2712-4d74-b5a1-b2883b3197ca" ; + crdch:id "69fe86c3-1e82-4583-9051-ffdb84224239" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c53d6135-c614-45f4-8f41-49b20ed4a549" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "ed5933bf-adaf-4bee-81fb-b1ec5782c248" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; - crdch:system "GDC" ] ; - crdch:text "N1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "49e46e5d-46b8-41f2-954e-c3c7b563a55b" ; + crdch:id "b5616ad7-8322-44c9-8b64-01314decc5a5" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-041937-203493_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-9df16b49-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:28:08.827884-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1108ef37-87b6-4b62-82f3-5e799fc4fb52" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "3dc819bf-5af3-4be1-a892-974d670975c9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24704,47 +24310,88 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "de3c2719-988d-4266-98cd-c1139a2cc412" ; + crdch:id "cbdf0116-28d4-42a0-ba6e-43a8587de68f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0006641-T01-IM5_diagnosis" ] ; + crdch:value "GENIE-DFCI-008605-9620_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "faf18ba4-6d92-4da3-bd43-5071bb88c5e1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; + crdch:system "GDC" ] ; + crdch:text "Malignant rhabdoid tumor" ] ; + crdch:id "d813126a-5e28-5c5a-8730-598f0d047584" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TARGET-52-PATBLF_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:system "GDC" ] ; + crdch:text "Lip" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:02:01.981535-05:00"^^ ] ] ; + crdch:text "8963/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4e6ffe6c-feee-4dca-b56d-0f2c8b498ae6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "ac3e795d-69a1-57f5-9dec-5b59e2523091" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Blood Derived Normal" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "eb5eeeae-6bd7-511e-9f13-51531684c774" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ; + crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:system "GDC" ] ; + crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "unknown" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "f1143020-2e95-4028-a2bf-c03a5ba6ea4e" ; + crdch:id "43aa2337-12ee-410b-9182-0de9352057f0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD14041_diagnosis" ] ; + crdch:value "AD3230_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:41:38.922504-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:59:56.723939-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fe72277e-ae77-486d-b5a9-844c483267eb" ; + crdch:id "900eabba-ab2e-4b0b-9738-db52f9203db9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; crdch:text "Metastatic" ] ; @@ -24758,71 +24405,68 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, spindle cell" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "509526cc-f60a-4e6d-8a18-2f76ba8e995c" ; + crdch:text "Squamous cell carcinoma, spindle cell" ] ; + crdch:id "d80aa9c7-2a22-57da-87ef-750dd4c0b494" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000586-T01-IM3_diagnosis" ] ; + crdch:value "TCGA-IQ-A61O_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8074/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "8074/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6d54051a-c75c-40e6-9215-3e470f0d242e" ; + crdch:id "09e8433c-1f86-42c5-91c0-2512fc4a7fe9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "a37311af-d40e-5c8f-ba14-b3b2ae22e486" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6997_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8b73f661-e1ec-4bcb-9eea-a5e66237229a" ; + crdch:id "eee85b30-6d16-4f53-aac1-b74f36a62d9a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b4c9a3aa-151e-478b-bc18-ce793b68ae09" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "00a721c6-6cb7-4408-a63a-6dae9310a3fe" ; + crdch:id "24e39735-725e-4627-82b6-c56ff33e3465" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; @@ -24837,60 +24481,45 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; - crdch:system "GDC" ] ; - crdch:text "T3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; - crdch:system "GDC" ] ; - crdch:text "N2c" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "89e61c6e-3fb5-494b-81b3-7280119fefc9" ; + crdch:id "601e60c5-25a1-41e7-a47e-2a069cb8e099" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-011185-11116_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD11228_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Nasopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T09:56:48.362532-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "25bebf87-88d5-4cd5-b2d7-3f2b7c1a0a02" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "b62623cd-3d81-4e48-bba4-7df880930106" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24901,20 +24530,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fbf35ed3-c5af-4591-88be-e9971b7d40f6" ; + crdch:id "2e4427b7-e557-49c7-85ef-39a02c4a441c" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-053418-203556_diagnosis" ] ; + crdch:value "GENIE-DFCI-050738-234120_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:20:30.865187-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:18:25.269226-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a3b9c3f7-8499-4c17-92f9-274b1ee52764" ; + crdch:id "c6e1507a-83f3-4c51-8275-319d0dcd8f97" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -24925,26 +24554,29 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "04081703-b701-4765-8309-0a204a48c183" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "583cb32e-5e1c-4f3a-bdef-035629e3eb57" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-VICC-201710-unk-1_diagnosis" ] ; + crdch:value "AD5451_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-28T12:01:45.147328-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:40:28.865821-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "cc51bca3-858a-4ac3-b48a-c4d273b2329c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "a8ae1d5d-04b7-4012-9bf5-70a664f325ee" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -24952,61 +24584,76 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "9d69f6a3-4edb-54e3-a840-ff1ff0aefb30" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "5976f296-bcb7-49a6-8db6-8620875f12e3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A7JK_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0008036-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Hypopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "257963cb-44bc-4946-ac72-7a1bb02f6af9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "90bcf4eb-dd05-5d4d-b666-6947b36143d8" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-D6-A6ES_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "90e4a976-0d97-47ef-aa29-295c2afeb31b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "0ebb072d-0596-4deb-8607-2548b0396fb0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "56c76698-7155-4f7a-9f9e-4fb62c673599" ; + crdch:id "59ddae84-32f9-40c0-9d9f-e3b883ab5c47" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "15776f80-0722-45a8-bc97-cc209cef631b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "f99dc3bf-e91d-4011-b62a-2653b53417f0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; @@ -25016,53 +24663,68 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ce63ab25-f6d3-475c-abca-986d8d91b869" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "562417d9-1094-45a9-9621-7fc5ce203ac3" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0019055-T01-IM6_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "AD2564_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:42:00.849990-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:00:26.233095-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b5793531-8ec1-4bd9-9544-57844ebee0a6" ; + crdch:id "4448e3e1-aeff-4ea0-82e4-1692b9b59414" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -25074,23 +24736,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "12d5265d-8eb5-4122-9e4d-976bdc0ded08" ; + crdch:id "5c70e571-fbe5-407f-aea2-9f740e6f5d2a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002469-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-DFCI-002399-7809_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Hypopharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:12:32.615882-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ed3acbbc-fb24-4be6-b09c-e0b6f4d9814f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "d57d8dd7-f0d5-4c3e-9ac7-cc23e2aa77d7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -25101,56 +24763,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "155420b6-0bc4-42f0-a28d-863e56f9e200" ; + crdch:id "d2a0bb97-195f-422a-969f-0342485cf8c6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD864_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-DFCI-010743-8938_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:58.520537-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "24318871-5bfe-4bbe-8df8-9e415558ae47" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "545abbb1-03c0-4b81-af21-3ebb7a5bb299" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD4812_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; - crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:53.493092-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4288c5a9-610c-4b1f-b102-2b96b49a6fd8" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "1f6b16e8-e1f4-462a-ac25-700c915f464f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -25158,28 +24787,25 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Adenocarcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Adenocarcinoma, NOS" ] ; - crdch:id "1c3027a0-7ae3-4ee6-a71d-b357ad841b3c" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "ea4330da-9d29-4e64-8197-55a50ee283dd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD4542_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "GENIE-MSK-P-0001557-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8140/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8140/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:06:20.797099-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "de90601b-1eda-4d1a-aa41-29feebdcfd57" ; + crdch:id "90c9d5f2-ca54-4084-99e7-e9407e364b12" ; crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; @@ -25191,19 +24817,26 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6788d692-193d-5d61-975f-1a79e54439ff" ; + crdch:id "c18fbc5a-880d-5f56-8466-527763c437d6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-6516_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "TCGA-CV-A45Z_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c129394b-3c04-4a6a-b4ea-d56d96bf28ef" ; + crdch:id "f844574a-cb7f-4f66-83d4-ee0ca41a63d1" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "fc3d6178-acc8-4e4f-b935-3cc1f6c0f304" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -25211,75 +24844,65 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c3c82c51-0200-44c8-b5aa-050084983398" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2d8d11be-421d-4f96-b5d6-4cbc632f11f3" ; + crdch:id "866bc103-c5bc-4365-8ef6-40064b33046d" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; - crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "not reported" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "Stage III" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "stage i" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; + crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ] ] . + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "73adb3fc-a3c9-487c-a0d0-fa8b09707932" ; + crdch:id "4c3c3952-6e85-4fd3-bc05-81c91ce3faef" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-005121-1375_diagnosis" ] ; + crdch:value "GENIE-DFCI-003978-789_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Hypopharynx" ; crdch:system "GDC" ] ; crdch:text "Hypopharynx" ] ] ; @@ -25290,7 +24913,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "eadf6e9a-c6c3-444c-8e93-8ab77ed87d09" ; + crdch:id "10935163-56ad-43d1-af91-1846aa5922eb" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -25301,22 +24924,29 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "b07c0682-d50b-5680-97fc-8e709e21c064" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "232f3bad-3cb2-5b4a-91e2-71f37a7eff72" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-D6-8568_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-UF-A71B_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:text "Gum" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8071/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c812093b-04ce-4d3f-841d-9b81de63fc38" ; + crdch:id "3a4af2fc-6443-4644-9da0-fee722e6d5c6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "df66e44f-3130-4d7b-a1d9-2d90f96b4c7e" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], @@ -25324,14 +24954,7 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "6f150e98-8b4e-44ee-953b-1692d76c8868" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "eac181d7-f8b8-4350-92aa-62d3fd1bd86b" ; + crdch:id "5c464f43-4aa0-4203-8828-5fc4cb13cf42" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -25341,96 +24964,111 @@ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; - crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "stage ii" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "Stage II" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; - crdch:id "f904a635-80a1-579a-8f1f-0aa288492b45" ; + crdch:id "bd9d72bf-8331-5bd7-a4bc-1522518d3fb7" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-BA-A8YP_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-A468_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Lip" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; crdch:text "8071/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4a339708-153a-4780-a265-70557765a754" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "66643338-ed21-460e-a1dc-b547c5b14500" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a9ebdedd-056f-4bc1-abc2-7089544a1549" ; + crdch:id "54fda578-dfb1-4a1b-8b01-2b7e9292f387" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e62166c3-871d-4b0f-999a-4f033d7cb6c7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:id "7dc1e99f-c601-48c2-8326-389d9f084e29" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; @@ -25439,76 +25077,129 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVB" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N3" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N3" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "T3" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "3f9d8932-dc6a-4225-b085-953225ae22ad" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0007407-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:06:12.185212-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "cd1a65bd-7bc3-4c1e-9d5e-792938c2fc5a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; - crdch:system "GDC" ] ; - crdch:text "stage ivb" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "6ca9116f-412c-41d9-872b-1775f3d9464c" ; + crdch:id "1d13cc0a-da04-5925-8930-693f09cd6432" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD11803_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-T2-A6X0_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:01:51.025011-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3dac18fb-752c-42aa-bdad-9f91d54fb950" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "6f085b6d-6abf-4d89-a17a-89e6c7f8fcc2" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Not Reported" ] ; + crdch:id "0416608e-19db-43b8-ac11-87406b0164d0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a4b8631d-80aa-4665-86b4-0caa7241da66" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:system "GDC" ] ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; @@ -25518,53 +25209,19 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4dbbefaa-8e8e-4a44-943b-48687f123673" ; + crdch:id "b7c4b294-1897-5001-8494-cedac0a7f991" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0010088-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CV-5440_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:13:38.880466-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b5da1115-1fe3-49a4-892b-ef43e64dbee4" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; - crdch:id "00ed54be-bd0c-5950-9165-b08535ef9f18" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-TN-A7HI_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; - crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; - crdch:system "GDC" ] ; - crdch:text "8072/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2a081426-e4fe-4868-adc9-c14142490b81" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "9808b586-4541-42a8-a72c-0c043ff568b3" ; + crdch:id "28780b51-0b53-4d73-b399-ec90b45de0d3" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], @@ -25572,10 +25229,17 @@ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3ad15aca-9197-4512-8bb9-77099ae8f049" ; + crdch:id "3f9a9578-e8e6-47b7-af7b-31d9cffbfd3a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d773747d-fd09-4890-a436-9b212e19063b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:system "GDC" ] ; + crdch:text "Solid Tissue Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; @@ -25585,134 +25249,128 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage I" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "83e6c6d4-83d7-55d8-ab82-aba8f3e543f5" ; + crdch:id "6ea3680f-baf2-53a3-8308-ae9dfd6ceb1e" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-6988_diagnosis" ] ; + crdch:value "TCGA-CN-5355_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4f72ee1e-37e2-4845-90de-812686a25980" ; + crdch:id "63535469-d402-4ba2-9ab5-986e6ed80f55" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5bf33753-d3c4-4fbe-a8e0-af958efb6fd1" ; + crdch:id "c2ef7833-c2fa-446c-a12e-f353c744b1e4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "ca2a45b4-1eb0-4e28-a4c8-5647bfbaa98c" ; + crdch:id "256d61e1-54c4-4250-bd17-5bb82496f5f4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; @@ -25723,147 +25381,131 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "bd3b2bda-4737-50bb-863a-334134a31156" ; + crdch:id "f351c260-09d7-594c-8347-292ae6f65f1f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-QK-A8ZA_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CN-A49B_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f92383bc-5869-44d6-a128-60b60043d778" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "4db7e146-bf2a-4729-ae80-d471370b62a0" ; + crdch:id "16b91d52-3168-44d9-bbbd-9f6e8b2582b6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "9adfbc71-da3c-4a8e-a72f-76690e90a8ca" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "a49128ea-01e4-4587-845b-6b26bafa1c29" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; crdch:system "GDC" ] ; crdch:text "MX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; - crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ] ] . + crdch:text "N1" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Malignant rhabdoid tumor" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Malignant rhabdoid tumor" ] ; - crdch:id "2e79ab38-e511-5e60-8c81-1584d28a909e" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "310c112e-7e2f-4987-a515-fe213ae70986" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TARGET-52-PASVDP_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Lip" ; + crdch:value "GENIE-MSK-P-0002198-T01-IM3_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Lip" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8963/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8963/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "a28e1682-4703-527b-bd4e-81f86fa6f35a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; - crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; - crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2016-02-17T11:50:17.531058-06:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "fd9ff1de-6856-5a42-ad32-2e3aa28dc2d7" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ; - crdch:specific_tissue_morphology [ crdch:coding [ crdch:code "Rhabdoid tumor (kidney) (RT)" ; + crdch:id "b9d46cb7-1679-4998-853f-03e5827cbb53" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Rhabdoid tumor (kidney) (RT)" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Unknown" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "unknown" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e980228b-ecef-406e-91da-09bc06d5ad04" ; + crdch:id "32bc08a5-7441-4dfc-b13c-9e193e5a7ac9" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-000968-1363_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0001682-T01-IM3_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:35:23.418160-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "37ecc052-0274-45dd-98db-fb0d5476fa16" ; + crdch:id "b2a64027-92cc-4961-9c27-821fff58c5ca" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -25874,29 +25516,26 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, undifferentiated, NOS" ] ; - crdch:id "4f1912bc-3704-49b0-b916-6d0e99463553" ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "fac35228-e5eb-403f-a9fd-c88a2518c7c1" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "AD5075_diagnosis" ] ; + crdch:value "GENIE-DFCI-009544-8452_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; crdch:system "GDC" ] ; - crdch:text "8020/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:07:48.972608-05:00"^^ ] ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "dbf24e2a-1a10-4dfb-be35-8021f82b947c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ; - crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "933ddbda-c8bb-4e81-9342-9d7379bd6332" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -25907,23 +25546,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4c9f5000-dbac-4497-b434-57036c18a022" ; + crdch:id "1137ba9a-12d3-4b2d-a3a4-d95de8bcf49a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008669-7093_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "GENIE-GRCC-8191e4ea-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "c0927894-b73f-4930-b147-e079caeb60e5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "783e6c97-20aa-4c8b-a7e1-ae0d8f7af28d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -25931,77 +25570,199 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "f3270d37-2d06-4867-973e-54e8ea28208b" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "589f8f36-79a2-513f-a83e-cd707818b834" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0002787-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:value "TCGA-HD-A634_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "c25592d6-b3d3-47b6-a3c5-3cbc81803152" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "1bae9a44-1ce3-45b1-9902-40faeba58120" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3eb1f15d-003c-42bc-8832-ea364ee8931b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "34c0ddaa-1fcf-4e5c-b5bf-7cfae596c09d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iva" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5cb1278d-4b33-401c-b200-b4408788c927" ; + crdch:id "21b7042c-de33-572f-a77e-98db817efd44" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-002669-7683_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-6492_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Palate" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4d69eeb9-81bd-4146-9a4a-3ca86c789272" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "2da6f33b-4a9f-4cf6-ad8f-873be656a6f8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "9d258494-fb84-4435-aa3a-f5778ac061c5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "47d4038e-908a-40b8-8a91-7bdcc4421624" ; + crdch:id "0ab5d8a1-108f-450c-89bd-efd0c4d285ea" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007857-7172_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0003059-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:50:42.610446-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "01a0cb84-c716-4134-aa16-ef008ae30469" ; + crdch:id "1303ddf5-cd55-47c9-9f93-c09d7bbf2f80" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -26012,166 +25773,354 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b7c8a51e-1403-54ce-a94e-ca7cfc05c21b" ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "022d6f9b-38da-5bfb-8bd9-e800361481a0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-HD-7754_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-D6-A6EK_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8071/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "adb496a1-07eb-45b9-8690-00184143300e" ; + crdch:id "0a64b28d-8dde-4eaf-bac5-217406cbc4c6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-23T13:20:20.149518-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "97d5f4b1-b8a5-4fb1-8af6-f0e6cfc302f6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "ad47c17b-e21c-4aed-aac6-8a062c6b5e42" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3fb86c71-0f8b-4022-b19f-d394401df9fe" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "b3a55bcd-1f88-4d25-9f95-5ef7393d6cf0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; + crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "f904a635-80a1-579a-8f1f-0aa288492b45" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-BA-A8YP_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:system "GDC" ] ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e62166c3-871d-4b0f-999a-4f033d7cb6c7" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a9ebdedd-056f-4bc1-abc2-7089544a1549" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "4a339708-153a-4780-a265-70557765a754" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "stage ivb" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; + crdch:system "GDC" ] ; + crdch:text "N3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVB" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N3" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ], + crdch:text "N3" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, keratinizing, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, keratinizing, NOS" ] ; + crdch:id "6739697d-d536-5d38-813f-5a4973a97cb9" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-CN-A49A_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Palate" ; + crdch:system "GDC" ] ; + crdch:text "Palate" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8071/3" ; + crdch:system "GDC" ] ; + crdch:text "8071/3" ] ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "8e00c51b-cc4e-4de3-ad9d-8ffe30f2ab0b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "77234a56-cad6-4b84-aabb-032be68f7dea" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVB" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVB" ; + crdch:system "GDC" ] ; + crdch:text "stage ivb" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4b" ; + crdch:system "GDC" ] ; + crdch:text "T4b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:system "GDC" ] ; + crdch:text "T4a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "T2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "N2b" ] ] ] . + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:system "GDC" ] ; + crdch:text "N0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5b91d8ab-6ed3-4c0a-a56b-8f0e151eaf5a" ; + crdch:id "1e1fa97c-cb95-5810-9f22-9af6a0a42ce2" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-000195-4559_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-CR-6480_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "52beca45-8506-41fa-b0a0-3a8c24c9d7fe" ; + crdch:id "0c6b4631-381e-4b73-ac9e-62bbc1849ff4" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "ad342355-cfa9-458f-8723-7a099368b797" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008794-7198_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "536ca98b-7415-49d8-84c2-dca4b5070ff6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "e49031dd-14f3-4f2c-8457-d0249c491ae9" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:system "GDC" ] ; + crdch:text "N2a" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "fd3fbe29-2fa3-41f7-99c9-51d3d05ff5b4" ; + crdch:id "28fc2416-e276-4a4c-963f-1ff59d64fb44" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-003147-99_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "GENIE-GRCC-a947c792-sample-a_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-02T18:01:58.729859-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "13654c9a-afcc-4635-9885-8418a318ac7a" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "cb69d223-6e16-4e94-8a35-b1197a261b19" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Not Reported" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -26182,23 +26131,23 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "1fe06c82-aa43-44ac-a091-8dec17e796ba" ; + crdch:id "81d9c62a-5f07-4409-aad8-4f9e02b90669" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037687-158970_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0015745-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:26:11.717995-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "98e2382a-2d7b-445d-83ff-1dc53d66db12" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "cd31b18a-5019-4a94-8966-a1160e544684" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -26209,20 +26158,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "3439abcc-0169-490c-8794-73e53b937d7c" ; + crdch:id "842d6984-7c03-4ab6-95db-42fa2ea699db" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-037577-74790_diagnosis" ] ; + crdch:value "GENIE-DFCI-010671-11105_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-25T12:05:51.637331-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.873530-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "4121fe4a-1ae9-41e4-954d-88c88d047d9c" ; + crdch:id "6f9eeaa3-8bd1-479c-a0fc-98317eb458dc" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -26233,173 +26182,158 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "e3d5bf4e-2856-5604-a086-3e4464a68c05" ; + crdch:text "Squamous cell carcinoma, large cell, nonkeratinizing, NOS" ] ; + crdch:id "11688639-0783-576d-ac58-40e8e3a19be6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A7JF_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CN-A49C_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Tonsil" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8072/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; + crdch:text "8072/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7ce8968e-f693-4fa2-945a-0cea27c96ede" ; + crdch:id "7758f04c-0e07-4e8a-882d-ece76469f433" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f4e12699-7e71-42ba-994a-c3a9a71a95cb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "f4cf2a66-8872-41ee-8270-296d5f76265f" ; + crdch:id "34b36112-f260-4bf4-90b7-0cebc5988b59" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2a" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "N2a" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4e9b9fad-2d73-4867-b7f8-8e42769ea41e" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-009088-5942_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:43.308719-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "cc6054a8-ec09-42af-be24-4041b7be75cc" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "c1dc41f5-0fea-42e8-afdb-fabc542d0548" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0005869-T01-IM5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:58:03.635432-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "bb6ae997-ee6b-42e0-ab0c-c9fbc64f8d9b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; - crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "f50b7ab8-f114-470f-81b0-35ddd9246c46" ; + crdch:id "c061cf11-1e3a-5906-b58b-2b5530a456fd" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-034356-130499_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:value "TCGA-BA-6870_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; + crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-23T13:20:20.149518-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "21a0707d-357c-4ea4-aec8-1227b8997cbb" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:id "cc1be5d1-ea6a-4e7d-822b-51887dab88b6" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Metastatic" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "5bf05a41-3a19-445b-96bd-439b9cac01eb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e6af426a-d899-44ef-96a8-92bd76a0ea3a" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:system "GDC" ] ; + crdch:text "TX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2c" ; + crdch:system "GDC" ] ; + crdch:text "N2c" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M1" ; + crdch:system "GDC" ] ; + crdch:text "M1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVC" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVC" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:system "GDC" ] ; + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; @@ -26409,112 +26343,119 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "126d74e6-2981-5aea-80e7-62ec5cff609a" ; + crdch:id "ea23b8a9-c2fd-5392-8625-a26662cdf0ef" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CN-4739_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "TCGA-CR-7404_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; + crdch:text "Tonsil" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "f450dbe6-4972-4c49-af97-963bcd0d0da0" ; + crdch:id "a39131b9-e7c7-4385-a1b9-d8a0a0950337" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "b916fa4a-1d15-4619-9d6c-1000e96b7e0d" ; + crdch:id "a0723862-62f9-4770-b415-e8f52c447e7a" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "9491d6f0-1e3e-48e5-aabb-87704511904b" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Blood Derived Normal" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "NX" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "N2b" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; - crdch:system "GDC" ] ; - crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], + crdch:text "TX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; - crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "de59133c-2442-490c-9f22-057c8a47ff70" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0008518-T01-IM5_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; + crdch:system "GDC" ] ; + crdch:text "Oropharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T04:09:54.181448-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "f4e28471-79a4-456e-bba8-db331560bdb0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ] ] . + crdch:text "not reported" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d078cccf-6335-4c55-8d5e-a36e32dd8006" ; + crdch:id "9b75ffac-0af8-40a0-9cc6-8472fbe942ef" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-004034-372_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0015763-T01-IM6_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:22:15.693629-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:46:25.150285-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "7d1a8a2e-c9d3-4e1d-b183-3c82de7e2306" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "d02e5c34-3c1e-4a7d-a67d-c2525ac3a734" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -26525,9 +26466,9 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "b56e8d53-a875-5676-8d2d-f095f8b899af" ; + crdch:id "b9143400-abdf-5f03-9771-ebafe5bb5d43" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-CV-5444_diagnosis" ] ; + crdch:value "TCGA-CR-7371_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; @@ -26537,94 +26478,89 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "61380e29-a7ae-4e29-b69a-d56f234f1ba0" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; + crdch:id "5a5005d4-6cd9-431a-89ec-ce6d34b0fc7d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Solid Tissue Normal" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "8cc840ea-3053-41a2-a325-6e86f3deeec6" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "4deea4a5-4d54-48b2-9a46-68eea668283b" ; + crdch:id "ac9f5493-c06b-40dd-b80d-7be718d27289" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; crdch:system "GDC" ] ; - crdch:text "N1" ] ], + crdch:text "T3" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "Stage III" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T3" ; + crdch:system "GDC" ] ; + crdch:text "T3" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:text "M0" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . + crdch:text "Stage III" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "5d448af8-7478-4252-9043-772077929480" ; + crdch:id "03f214c1-e688-473f-b84b-5864f56a6a3a" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-023766-23966_diagnosis" ] ; + crdch:value "GENIE-DFCI-001000-1570_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:44.678712-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:06:57.341931-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "a3ca3ea8-6ea0-4585-8a50-294ca4c87a24" ; + crdch:id "016681b7-82cb-404f-a175-8cb6d3f6bc62" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -26635,64 +26571,80 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Basaloid squamous cell carcinoma" ; +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; - crdch:text "Basaloid squamous cell carcinoma" ] ; - crdch:id "35c83c03-b2ab-5f6b-a231-66a3f879a217" ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "0b9b2b22-2fe6-5569-99ea-4647a15e68a0" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-P3-A5Q5_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; + crdch:value "TCGA-CV-7177_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; - crdch:text "Tonsil" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8083/3" ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; - crdch:text "8083/3" ] ; + crdch:text "8070/3" ] ; crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3f5cd265-0dd3-40c3-94b8-e92d18ce87b0" ; + crdch:id "768e2bab-347b-4d90-887f-bf5692a91eb0" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "3b3502ab-ab9f-49d7-be08-243a7022463f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "21152590-1224-410e-aaf7-4088302c809f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ], + crdch:text "Blood Derived Normal" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "2e1b4cf3-61fe-452c-b800-f9bc53333713" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:id "ddb758e6-20a8-4a28-ba98-798de978154f" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:text "Solid Tissue Normal" ] ], + [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "e850a80d-1b50-4ab6-ab36-1d1a5e697d7e" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; + crdch:system "GDC" ] ; + crdch:text "7th" ] ; + crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage I" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:text "Stage I" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "Stage IVA" ] ], + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "T1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], + crdch:text "Stage II" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage II" ; + crdch:system "GDC" ] ; + crdch:text "stage ii" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Pathological Tumor (T)" ] ; @@ -26702,75 +26654,36 @@ [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; - crdch:text "MX" ] ], + crdch:text "N0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2" ; - crdch:system "GDC" ] ; - crdch:text "N2" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; - crdch:system "GDC" ] ; - crdch:text "stage iva" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9233f502-9580-4801-915e-732ca0f26a2c" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-050720-203425_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; - crdch:system "GDC" ] ; - crdch:text "Oropharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:18:25.269226-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "c1353660-3a6c-4a01-8800-d52a40b6ed68" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . + crdch:text "NX" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "4943c82a-30d2-4c85-a233-032a49ca801d" ; + crdch:id "c5df4db4-06f3-4596-98d2-3ab0e5df45b6" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-008342-5809_diagnosis" ] ; + crdch:value "GENIE-MSK-P-0003711-T01-IM5_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:54:19.535598-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "e01da120-9c9d-4ef7-8568-525f74222dd5" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "7eef7c3e-d42d-4cf5-9ad1-3099b828f776" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -26778,53 +26691,29 @@ crdch:system "GDC" ] ; crdch:text "not reported" ] ] ] . -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, undifferentiated, NOS" ; crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "43212ae1-0d0a-411e-8ae0-61de91147afe" ; + crdch:text "Carcinoma, undifferentiated, NOS" ] ; + crdch:id "c740d9c9-bb4f-4ae0-9920-43267c9bc180" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-006740-7890_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:value "AD14561_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8020/3" ; crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; + crdch:text "8020/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2017-06-01T10:42:22.825295-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5f316e98-9980-4841-b297-f07b3e87004f" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9076e2ad-9cef-4efc-99d7-387d250445ee" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-025889-116451_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; - crdch:system "GDC" ] ; - crdch:text "Larynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; - crdch:system "GDC" ] ; - crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-06-03T15:37:30.937085-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:id "97cac184-023d-4aaf-9637-cc34969471cb" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "678dfc0e-f085-4c85-b444-8fc1604bdcfe" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:text "Metastatic" ] ; + crdch:tumor_status_at_collection [ crdch:coding [ crdch:code "Metastatic" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Metastatic" ] ] ; crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; @@ -26835,47 +26724,20 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "9d41e68e-c648-42ea-9320-6e08b9b5dd4c" ; + crdch:id "9eeeccb6-c3a5-4008-a87c-006d2e1efa9f" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-DFCI-007598-4084_diagnosis" ] ; + crdch:value "GENIE-DFCI-008672-7091_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Oropharynx" ; crdch:system "GDC" ] ; crdch:text "Oropharynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T18:54:47.858087-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "87d18b2c-1241-43b3-b7aa-24442a047ade" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; - crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "not reported" ] ] ] . - -[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; - crdch:system "GDC" ] ; - crdch:text "Carcinoma, NOS" ] ; - crdch:id "68a8cfd1-e890-4bd7-931b-33636e8cf10b" ; - crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "GENIE-MSK-P-0000668-T01-IM3_diagnosis" ] ; - crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; - crdch:system "GDC" ] ; - crdch:text "Nasopharynx" ] ] ; - crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; - crdch:system "GDC" ] ; - crdch:text "8010/3" ] ; - crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-10-03T03:31:25.700438-05:00"^^ ] ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:56:40.150348-05:00"^^ ] ] ; crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "5c9ff077-5620-4611-a58c-fdd8ed98b2db" ; + crdch:id "6db9d94f-7868-4a64-b9b4-a5b95747c317" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ] ; @@ -26889,37 +26751,37 @@ [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "d9cc35a1-8103-5f6b-8d97-cc64c564c677" ; + crdch:id "b56e8d53-a875-5676-8d2d-f095f8b899af" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-UF-A7JH_diagnosis" ] ; + crdch:value "TCGA-CV-5444_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; crdch:system "GDC" ] ; crdch:text "Larynx" ] ] ; crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; crdch:system "GDC" ] ; crdch:text "8070/3" ] ; - crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "2b803b39-f13c-4335-9845-05bb61830015" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:text "Not Reported" ] ; + crdch:id "4deea4a5-4d54-48b2-9a46-68eea668283b" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], + crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "980726e2-9e0c-4212-b5aa-69e139fc3be7" ; + crdch:id "8cc840ea-3053-41a2-a325-6e86f3deeec6" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "1c9d867a-6fba-49a1-99ba-63bd01942397" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:id "61380e29-a7ae-4e29-b69a-d56f234f1ba0" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Solid Tissue Normal" ; crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; + crdch:text "Solid Tissue Normal" ] ] ; crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; crdch:system "GDC" ] ; crdch:text "7th" ] ; @@ -26929,61 +26791,55 @@ crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; crdch:text "T4a" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; crdch:system "GDC" ] ; - crdch:text "stage iva" ] ], + crdch:text "T4a" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; crdch:system "GDC" ] ; crdch:text "N0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Metastasis (M)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; - crdch:system "GDC" ] ; - crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; crdch:system "GDC" ] ; crdch:text "Pathological Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; - crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "N0" ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; - crdch:text "N0" ] ], + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; crdch:system "GDC" ] ; crdch:text "Clinical Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; - crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; - crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4a" ; - crdch:system "GDC" ] ; - crdch:text "T4a" ] ] ] . + crdch:text "M0" ] ] ] . [] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; crdch:system "GDC" ] ; crdch:text "Squamous cell carcinoma, NOS" ] ; - crdch:id "0a622048-699a-55f4-ba31-6c9e95e1cabd" ; + crdch:id "5202e65a-e9af-58ee-8960-9190089fb197" ; crdch:identifier [ crdch:system "GDC-submitter-id" ; - crdch:value "TCGA-DQ-7590_diagnosis" ] ; + crdch:value "TCGA-CR-6467_diagnosis" ] ; crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Tonsil" ; crdch:system "GDC" ] ; crdch:text "Tonsil" ] ] ; @@ -26993,68 +26849,212 @@ crdch:related_specimen [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "36fb3f52-714b-4b86-a7a5-ca4b017fd182" ; + crdch:id "5ef4d047-5a84-4e03-acf5-02029d8a4cf2" ; crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; crdch:system "GDC" ] ; crdch:text "Primary Tumor" ] ], [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; crdch:system "GDC" ] ; crdch:text "Not Reported" ] ; - crdch:id "95018dba-f23d-4af0-b774-c28be60007f7" ; + crdch:id "2d9ad43c-f177-455e-9b63-1b9ffdc672d9" ; crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; crdch:system "GDC" ] ; - crdch:text "Blood Derived Normal" ] ], - [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; - crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; - crdch:system "GDC" ] ; - crdch:text "Not Reported" ] ; - crdch:id "b8eb9edb-fce8-4e72-9cbf-c4868c04965c" ; - crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; - crdch:system "GDC" ] ; - crdch:text "Primary Tumor" ] ] ; - crdch:stage [ crdch:method_type [ crdch:coding [ crdch:code "AJCC staging system 7th edition" ; - crdch:system "GDC" ] ; - crdch:text "7th" ] ; - crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; crdch:text "Clinical Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "T1" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; crdch:system "GDC" ] ; - crdch:text "T1" ] ], + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; crdch:system "GDC" ] ; crdch:text "Overall" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; crdch:system "GDC" ] ; - crdch:text "not reported" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:text "stage iii" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; - crdch:text "Clinical Metastasis (M)" ] ; + crdch:text "Clinical Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; + crdch:system "GDC" ] ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T2" ; + crdch:system "GDC" ] ; + crdch:text "T2" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Node (N)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N1" ; + crdch:system "GDC" ] ; + crdch:text "N1" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; crdch:system "GDC" ] ; crdch:text "M0" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage III" ; + crdch:system "GDC" ] ; + crdch:text "Stage III" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "671671bc-dbf4-4e15-b978-6aceaac1533f" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-MSK-P-0016761-T01-IM6_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Larynx" ; + crdch:system "GDC" ] ; + crdch:text "Larynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2019-05-31T18:17:41.081467-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "0d989563-7a49-49e9-9417-4b607d661ab4" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Metastatic" ; + crdch:system "GDC" ] ; + crdch:text "Metastatic" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Squamous cell carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Squamous cell carcinoma, NOS" ] ; + crdch:id "28979d39-3da1-556a-9b82-2a9953b57989" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "TCGA-P3-A5QF_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Gum" ; + crdch:system "GDC" ] ; + crdch:text "Gum" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8070/3" ; + crdch:system "GDC" ] ; + crdch:text "8070/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-05-17T12:19:46.292188-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "2e51af26-4d06-4b66-be71-0bebed2e4557" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "d30d7d4c-0acf-4b61-9d7e-2c15e20d73a8" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ], + [ crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "903ed81a-057c-41ad-93de-aaa9d9c082c5" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Blood Derived Normal" ; + crdch:system "GDC" ] ; + crdch:text "Blood Derived Normal" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Node (N)" ; crdch:system "GDC" ] ; crdch:text "Clinical Node (N)" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; + crdch:system "GDC" ] ; + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "MX" ; + crdch:system "GDC" ] ; + crdch:text "MX" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Overall" ; crdch:system "GDC" ] ; crdch:text "Clinical Overall" ] ; crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; crdch:system "GDC" ] ; crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "stage iva" ] ], [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Node (N)" ; crdch:system "GDC" ] ; crdch:text "Pathological Node (N)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "NX" ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "N2b" ; crdch:system "GDC" ] ; - crdch:text "NX" ] ], - [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Tumor (T)" ; + crdch:text "N2b" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Tumor (T)" ; crdch:system "GDC" ] ; - crdch:text "Pathological Tumor (T)" ] ; - crdch:value_codeable_concept [ crdch:coding [ crdch:code "TX" ; + crdch:text "Clinical Tumor (T)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "T4" ; crdch:system "GDC" ] ; - crdch:text "TX" ] ] ] . + crdch:text "T4" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Pathological Overall" ; + crdch:system "GDC" ] ; + crdch:text "Pathological Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Stage IVA" ; + crdch:system "GDC" ] ; + crdch:text "Stage IVA" ] ], + [ crdch:observation_type [ crdch:coding [ crdch:code "Clinical Metastasis (M)" ; + crdch:system "GDC" ] ; + crdch:text "Clinical Metastasis (M)" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "M0" ; + crdch:system "GDC" ] ; + crdch:text "M0" ] ] ] . + +[] crdch:condition [ crdch:coding [ crdch:code "Carcinoma, NOS" ; + crdch:system "GDC" ] ; + crdch:text "Carcinoma, NOS" ] ; + crdch:id "1d93a53e-6030-43c7-b479-9faa6fc8febf" ; + crdch:identifier [ crdch:system "GDC-submitter-id" ; + crdch:value "GENIE-DFCI-002633-5917_diagnosis" ] ; + crdch:metastatic_site [ crdch:site [ crdch:coding [ crdch:code "Nasopharynx" ; + crdch:system "GDC" ] ; + crdch:text "Nasopharynx" ] ] ; + crdch:morphology [ crdch:coding [ crdch:code "8010/3" ; + crdch:system "GDC" ] ; + crdch:text "8010/3" ] ; + crdch:related_specimen [ crdch:creation_activity [ crdch:date_ended [ crdch:date_time "2018-09-24T17:18:52.539095-05:00"^^ ] ] ; + crdch:general_tissue_morphology [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "Not Reported" ] ; + crdch:id "a8ec3306-0190-4e13-94d1-e269b8479a1d" ; + crdch:source_material_type [ crdch:coding [ crdch:code "Primary Tumor" ; + crdch:system "GDC" ] ; + crdch:text "Primary Tumor" ] ] ; + crdch:stage [ crdch:observations [ crdch:observation_type [ crdch:coding [ crdch:code "Overall" ; + crdch:system "GDC" ] ; + crdch:text "Overall" ] ; + crdch:value_codeable_concept [ crdch:coding [ crdch:code "Not Reported" ; + crdch:system "GDC" ] ; + crdch:text "not reported" ] ] ] . diff --git a/poetry.lock b/poetry.lock index 209812c..c7ad27a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -24,11 +24,11 @@ python-versions = "*" [[package]] name = "argcomplete" -version = "1.12.3" +version = "2.0.0" description = "Bash tab completion for argparse" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.6" [package.dependencies] importlib-metadata = {version = ">=0.23,<5", markers = "python_version == \"3.7\""} @@ -38,20 +38,36 @@ test = ["coverage", "flake8", "pexpect", "wheel"] [[package]] name = "argon2-cffi" -version = "21.1.0" +version = "21.3.0" description = "The secure Argon2 password hashing algorithm." category = "main" optional = false -python-versions = ">=3.5" +python-versions = ">=3.6" [package.dependencies] -cffi = ">=1.0.0" +argon2-cffi-bindings = "*" +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest", "sphinx", "furo", "wheel", "pre-commit"] -docs = ["sphinx", "furo"] +dev = ["pre-commit", "cogapp", "tomli", "coverage[toml] (>=5.0.2)", "hypothesis", "pytest", "sphinx", "sphinx-notfound-page", "furo"] +docs = ["sphinx", "sphinx-notfound-page", "furo"] tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] +[[package]] +name = "argon2-cffi-bindings" +version = "21.2.0" +description = "Low-level CFFI bindings for Argon2" +category = "main" +optional = false +python-versions = ">=3.6" + +[package.dependencies] +cffi = ">=1.0.1" + +[package.extras] +dev = ["pytest", "cogapp", "pre-commit", "wheel"] +tests = ["pytest"] + [[package]] name = "argparse" version = "1.4.0" @@ -70,17 +86,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "attrs" -version = "21.2.0" +version = "21.4.0" description = "Classes Without Boilerplate" category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [package.extras] -dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit"] +dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "furo", "sphinx", "sphinx-notfound-page", "pre-commit", "cloudpickle"] docs = ["furo", "sphinx", "zope.interface", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface"] -tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins"] +tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "zope.interface", "cloudpickle"] +tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "mypy", "pytest-mypy-plugins", "cloudpickle"] [[package]] name = "babel" @@ -105,7 +121,7 @@ python-versions = "*" name = "black" version = "21.12b0" description = "The uncompromising code formatter." -category = "main" +category = "dev" optional = false python-versions = ">=3.6.2" @@ -118,10 +134,7 @@ platformdirs = ">=2" tokenize-rt = {version = ">=3.2.0", optional = true, markers = "extra == \"jupyter\""} tomli = ">=0.2.6,<2.0.0" typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\" and implementation_name == \"cpython\""} -typing-extensions = [ - {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}, - {version = "!=3.10.0.1", markers = "python_version >= \"3.10\""}, -] +typing-extensions = ">=3.10.0.0" [package.extras] colorama = ["colorama (>=0.4.3)"] @@ -145,11 +158,11 @@ webencodings = "*" [[package]] name = "cachetools" -version = "4.2.4" +version = "5.0.0" description = "Extensible memoizing collections and decorators" category = "main" optional = false -python-versions = "~=3.5" +python-versions = "~=3.7" [[package]] name = "certifi" @@ -183,7 +196,7 @@ rdflib = ">=0.4.2" [[package]] name = "charset-normalizer" -version = "2.0.7" +version = "2.0.10" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false @@ -210,14 +223,14 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" [[package]] name = "crdch-model" -version = "1.1.5" +version = "1.2" description = "CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH). This Python package contains the dataclasses necessary to build and operate over data objects according to the CRDC-H model." category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.7.1,<3.10" [package.dependencies] -linkml-runtime = ">=1.1.2,<2.0.0" +linkml-runtime = ">=1.1.12,<2.0.0" [[package]] name = "debugpy" @@ -283,7 +296,7 @@ python-versions = ">=3.6" [[package]] name = "frozendict" -version = "2.0.7" +version = "2.1.3" description = "A simple immutable dictionary" category = "main" optional = false @@ -291,7 +304,7 @@ python-versions = ">=3.6" [[package]] name = "graphviz" -version = "0.18.2" +version = "0.19.1" description = "Simple Python interface for Graphviz" category = "main" optional = false @@ -300,7 +313,7 @@ python-versions = ">=3.6" [package.extras] dev = ["tox (>=3)", "flake8", "pep8-naming", "wheel", "twine"] docs = ["sphinx (>=1.8)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"] -test = ["pytest (>=6)", "pytest-mock (>=3)", "mock (>=4)", "pytest-cov"] +test = ["pytest (>=6)", "pytest-mock (>=3)", "mock (>=4)", "pytest-cov", "coverage"] [[package]] name = "greenlet" @@ -339,11 +352,11 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.2.0" +version = "4.10.0" description = "Read metadata from Python packages" category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""} @@ -351,7 +364,8 @@ zipp = ">=0.5" [package.extras] docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"] -testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] +perf = ["ipython"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" @@ -378,7 +392,7 @@ python-versions = "*" [[package]] name = "ipykernel" -version = "6.5.0" +version = "6.6.1" description = "IPython Kernel for Jupyter" category = "main" optional = false @@ -389,18 +403,19 @@ appnope = {version = "*", markers = "platform_system == \"Darwin\""} argcomplete = {version = ">=1.12.3", markers = "python_version < \"3.8.0\""} debugpy = ">=1.0.0,<2.0" importlib-metadata = {version = "<5", markers = "python_version < \"3.8.0\""} -ipython = ">=7.23.1,<8.0" +ipython = ">=7.23.1" jupyter-client = "<8.0" matplotlib-inline = ">=0.1.0,<0.2.0" +nest-asyncio = "*" tornado = ">=4.2,<7.0" traitlets = ">=5.1.0,<6.0" [package.extras] -test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "nose", "ipyparallel"] +test = ["pytest (!=5.3.4)", "pytest-cov", "flaky", "ipyparallel"] [[package]] name = "ipython" -version = "7.29.0" +version = "7.31.0" description = "IPython: Productive Interactive Computing" category = "main" optional = false @@ -460,7 +475,7 @@ test = ["pytest (>=3.6.0)", "pytest-cov", "mock"] [[package]] name = "isodate" -version = "0.6.0" +version = "0.6.1" description = "An ISO 8601 date/time/duration parser and formatter" category = "main" optional = false @@ -566,7 +581,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "jsonschema" -version = "4.2.1" +version = "4.3.3" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -577,6 +592,7 @@ attrs = ">=17.4.0" importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""} pyrsistent = ">=0.14.0,<0.17.0 || >0.17.0,<0.17.1 || >0.17.1,<0.17.2 || >0.17.2" +typing-extensions = {version = "*", markers = "python_version < \"3.8\""} [package.extras] format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"] @@ -600,7 +616,7 @@ qtconsole = "*" [[package]] name = "jupyter-client" -version = "7.0.6" +version = "7.1.0" description = "Jupyter protocol implementation and client libraries" category = "main" optional = false @@ -670,7 +686,7 @@ python-versions = ">=3.6" [[package]] name = "linkml" -version = "1.1.13" +version = "1.1.15" description = "Linked Open Data Modeling Language" category = "main" optional = false @@ -685,7 +701,7 @@ isodate = ">=0.6.0" jinja2 = "*" jsonasobj2 = ">=1.0.3,<2.0" jsonschema = ">=3.0.1" -linkml-runtime = ">=1.1.3,<1.1.4 || >1.1.4" +linkml-runtime = ">=1.1.9" linkml-runtime-api = "*" myst-parser = "*" openpyxl = "*" @@ -700,9 +716,10 @@ pyshex = ">=0.7.20" pyshexc = ">=0.8.3" python-dateutil = "*" pyyaml = ">=5.1,<6.0" -rdflib = ">=5.0,<6.0" -rdflib-jsonld = ">=0.5.0,<=0.6.1" 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= "linkml-runtime-api" @@ -751,7 +769,7 @@ linkml-runtime = "*" [[package]] name = "lxml" -version = "4.6.4" +version = "4.7.1" description = "Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API." category = "main" optional = false @@ -765,7 +783,7 @@ source = ["Cython (>=0.29.7)"] [[package]] name = "markdown-it-py" -version = "1.1.0" +version = "2.0.0" description = "Python port of markdown-it. Markdown parsing, done right!" category = "main" optional = false @@ -773,15 +791,17 @@ python-versions = "~=3.6" [package.dependencies] attrs = ">=19,<22" +mdurl = ">=0.1,<1.0" typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""} [package.extras] +benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"] code_style = ["pre-commit (==2.6)"] compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.2.2,<3.3.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "mistune (>=0.8.4,<0.9.0)", "panflute (>=1.12,<2.0)"] linkify = ["linkify-it-py (>=1.0,<2.0)"] plugins = ["mdit-py-plugins"] rtd = ["myst-nb (==0.13.0a1)", "pyyaml", "sphinx (>=2,<4)", "sphinx-copybutton", "sphinx-panels (>=0.4.0,<0.5.0)", "sphinx-book-theme"] -testing = ["coverage", "psutil", "pytest (>=3.6,<4)", "pytest-benchmark (>=3.2,<4.0)", "pytest-cov", "pytest-regressions"] +testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] [[package]] name = "markupsafe" @@ -804,20 +824,28 @@ traitlets = "*" [[package]] name = "mdit-py-plugins" -version = "0.2.8" +version = "0.3.0" description = "Collection of plugins for markdown-it-py" category = "main" optional = false python-versions = "~=3.6" [package.dependencies] -markdown-it-py = ">=1.0,<2.0" +markdown-it-py = ">=1.0.0,<3.0.0" [package.extras] code_style = ["pre-commit (==2.6)"] -rtd = ["myst-parser (==0.14.0a3)", "sphinx-book-theme (>=0.1.0,<0.2.0)"] +rtd = ["myst-parser (>=0.14.0,<0.15.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"] testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"] +[[package]] +name = "mdurl" +version = "0.1.0" +description = "Markdown URL utilities" +category = "main" +optional = false +python-versions = ">=3.6" + [[package]] name = "mistune" version = "0.8.4" @@ -830,13 +858,13 @@ python-versions = "*" name = "mypy-extensions" version = "0.4.3" description = "Experimental type system extensions for programs checked with the mypy typechecker." -category = "main" +category = "dev" optional = false python-versions = "*" [[package]] name = "myst-parser" -version = "0.15.2" +version = "0.16.1" description = "An extended commonmark compliant parser, with bridges to docutils & sphinx." category = "main" optional = false @@ -845,8 +873,8 @@ python-versions = ">=3.6" [package.dependencies] docutils = ">=0.15,<0.18" jinja2 = "*" -markdown-it-py = ">=1.0.0,<2.0.0" -mdit-py-plugins = ">=0.2.8,<0.3.0" +markdown-it-py = ">=1.0.0,<3.0.0" +mdit-py-plugins = ">=0.3.0,<0.4.0" pyyaml = "*" sphinx = ">=3.1,<5" @@ -858,7 +886,7 @@ testing = ["beautifulsoup4", "coverage", "docutils (>=0.17.0,<0.18.0)", "pytest [[package]] name = "nbclient" -version = "0.5.8" +version = "0.5.9" description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor." category = "main" optional = false @@ -877,7 +905,7 @@ test = ["codecov", "coverage", "ipython", "ipykernel", "ipywidgets", "pytest (>= [[package]] name = "nbconvert" -version = "6.3.0" +version = "6.4.0" description = "Converting Jupyter Notebooks" category = "main" optional = false @@ -925,7 +953,7 @@ test = ["check-manifest", "fastjsonschema", "testpath", "pytest", "pytest-cov"] [[package]] name = "nest-asyncio" -version = "1.5.1" +version = "1.5.4" description = "Patch asyncio to allow nested event loops" category = "main" optional = false @@ -963,7 +991,7 @@ test = ["pytest", "coverage", "requests", "nbval", "selenium", "pytest-cov", "re [[package]] name = "numpy" -version = "1.21.4" +version = "1.21.5" description = "NumPy is the fundamental package for array computing with Python." category = "main" optional = false @@ -993,7 +1021,7 @@ pyparsing = ">=2.0.2,<3.0.5 || >3.0.5" [[package]] name = "pandas" -version = "1.3.4" +version = 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optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" @@ -1069,11 +1096,11 @@ python-versions = "*" [[package]] name = "platformdirs" -version = "2.4.0" +version = "2.4.1" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." -category = "main" +category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.extras] docs = ["Sphinx (>=4)", "furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)"] @@ -1138,7 +1165,7 @@ twisted = ["twisted"] [[package]] name = "prompt-toolkit" -version = "3.0.22" +version = "3.0.24" description = "Library for building powerful interactive command lines in Python" category = "main" optional = false @@ -1173,7 +1200,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "pydantic" -version = "1.8.2" +version = "1.9.0" description = "Data validation and settings management using python 3.6 type hinting" category = "main" optional = false @@ -1188,7 +1215,7 @@ email = ["email-validator (>=1.0.3)"] [[package]] name = "pygments" -version = "2.10.0" +version = "2.11.1" description = "Pygments is a syntax highlighting package written in Python." category = "main" optional = false @@ -1196,7 +1223,7 @@ python-versions = ">=3.5" [[package]] name = "pyjsg" -version = "0.11.6" +version = "0.11.9" description = "Python JSON Schema Grammar interpreter" category = "main" optional = false @@ -1341,7 +1368,7 @@ python-versions = "*" [[package]] name = "pywin32" -version = "302" +version = "303" description = "Python for Window Extensions" category = "main" optional = false @@ -1377,7 +1404,7 @@ py = {version = "*", markers = "implementation_name == \"pypy\""} [[package]] name = "qtconsole" -version = "5.2.0" +version = "5.2.2" description = "Jupyter Qt console" category = "main" optional = false @@ -1399,11 +1426,17 @@ test = ["flaky", "pytest", "pytest-qt"] [[package]] 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">=3.7.1,<3.10" linkml = "^1.1.13" jsonschema = "^4.2.1" jupyter = "^1.0.0" pytest = "^6.2.5" PyLD = "^2.0.3" pip = "^21.3.1" -crdch-model = "^1.1.5" +crdch-model = "^1.2" pandas = "^1.3.4" [tool.poetry.dev-dependencies]