Pre-cancer colorectal polyps: HTAN Vanderbilt dataset. Chen et al. Cell 2021

[rmadupuri]

Fixes #1915
Testing Instance:
Triage Portal: https://triage.cbioportal.mskcc.org/study/summary?id=crc_hta11_htan_2021
Private Portal: https://private.cbioportal.mskcc.org/study/summary?id=crc_hta11_htan_2021

Curation and transformation of Pre-cancer HTAN CRC Vanderbilt Dataset:

Data collection:

• Data Source: Data on HTAN Portal
• Reference publication: PubMed Reference
• Reference genome used: GRCh37 for WXS and GRCh38 for scRNA-seq

Sample size selection

• Discovery set samples were used to generate the study (27 polyps). 15 samples were whole exome sequenced. All 27 samples went though scRNA-seq exp analysis.
• We can extend the cohort with Validation set samples if needed.

Clinical data

• Patient-Level Data: Table S1, Participants tab in HTAN Portal
• Sample-Level Data:Table S1, Biospecimens tab in HTAN Portal

Mutation data

• The Level 3 Bulk DNA filtered data files were obtained from the Vanderbilt team.
• Variants were annotated using Genome Nexus.

scRNA-seq data

• The Discovery set h5ad files for both epithelial and non-epithelial cells were used from cellxgene
  • Files used: Discovery (DIS) set of human colorectal tumor: Epithelial && VAL and DIS datasets: Non-Epithelial
• The absolute and relative cell frequencies in Generic Assay format were calculated
• The pseudo bulk RNA expression counts per sample was calculated from scRNA-seq by averaging the values across the cells.
• The script to generate the absolute, relative cell freq and pseudo bulk RNA-seq data from h5ad files : https://gist.github.com/rmadupuri/ffcdd2c753e28fd057a9c4bebf0fd9ca
• Zscores were calculated on pseudo bulk RNA by log transforming the data.

Imaging data

• H&E data was available for 24 samples: H&E tab
• MxIF images were available for 23 samples: MxIF tab. Multiple images were available per sample and as we do not support this, the images were split to multiple tabs for now as MxIF Image 1, 2, 3..