Public Data: TCGA Colon and Rectal Cancer

We are pleased to announce that data from the following paper have been made available on GenomeSpace: 

The Cancer Genome Atlas Network.  Comprehensive Molecular Characterization of Human Colon and Rectal Cancer. Nature. 2012;487:330-337. [doi:10.1038/nature11252]

The GenomeSpace mirror of this dataset includes all public level 3 and level 4 data from https://tcga-data.nci.nih.gov/docs/publications/coadread_2012/

You can access the data in GenomeSpace at the path /Public/SharedData/Datasets/TCGA/Colon and Rectal/.  (This requires a GenomeSpace login. If you don't have one, it's easy to register.)

Abstract:

To characterize somatic alterations in colorectal carcinoma (CRC), we conducted genome-scale analysis of 276 samples, analyzing exome sequence, DNA copy number, promoter methylation, mRNA and microRNA expression. A subset (97) underwent low-depth-of-coverage whole-genome sequencing. 16% of CRC have hypermutation, three quarters of which have the expected high microsatellite instability (MSI), usually with hypermethylation and MLH1 silencing, but one quarter has somatic mismatch repair gene mutations. Excluding hypermutated cancers, colon and rectum cancers have remarkably similar patterns of genomic alteration. Twenty-four genes are significantly mutated. In addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9, and FAM123B/WTX. Recurrent copy number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive CRC and important role for MYC-directed transcriptional activation and repression.