TCGA Pan-Cancer Atlas Colorectal Adenocarcinoma 2018

Overview

The TCGA Pan-Cancer Atlas colorectal adenocarcinoma cohort, accessed via cBioPortal, comprising 526 cases profiled with whole-exome sequencing, RNA-seq, and SNP arrays as part of the broader TCGA Pan-Cancer Atlas initiative. Widely used as a reference cohort for copy number, mutation frequency, and survival analyses in colorectal cancer.

Composition

  • 526 colorectal adenocarcinoma (COADREAD) cases.
  • Includes colon (COAD) and rectal (READ) adenocarcinomas.
  • Multi-omic profiling: whole-exome sequencing, copy number (SNP array), RNA-seq.
  • Accessible via cBioPortal.

Assays / panels (linked)

  • Whole-exome sequencing (WES)
  • RNA-seq
  • SNP array (copy number)

Papers using this cohort

  • PMID:36334560 — Bioinformatic analysis of FBXO7 copy number loss in CRC; 526 cases used for copy number, expression, and survival analyses.

Notable findings derived from this cohort

  • FBXO7 shallow deletions (heterozygous loss) occur in 32.5% (169/526) of CRC cases; deep deletions are rare (<0.2%); FBXO7 shallow deletions associate with increased genome instability (fraction altered, aneuploidy score, tumor break load; q < 0.0001) and worse overall, progression-free, and disease-specific survival (log rank, p < 0.05) PMID:36334560.
  • MC3 ensemble mutation calls (7 callers, 10,510 TCGA tumor/normal pairs, 33 cancer types) form the somatic-variant backbone of this PanCanAtlas cBioPortal study PMID:29596782
  • Pan-cancer aneuploidy analysis of 10,522 TCGA tumors used this cohort as part of the gastrointestinal cluster (COAD/READ) analysis of arm-level copy-number alterations PMID:29622463

Sources

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