Cell. Volume 158: 929-944, 14 August 2014 10.1016/g.cell.2014.06.049
Recent genomic analyses of pathologically defined tumor types identify ‘‘within-a-tissue’’ disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All data sets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (12 Files)
Supplemental Data
The following are input data and output data (cluster assignments) for 6 platforms:
| Platform | Input Data | Subtype Assignments |
|---|---|---|
| mRNAseq | rnaseq_input.txt | rnaseq_output.txt |
| miRNAseq | mirna_input.csv | mirna_output.txt |
| Somatic Copy Number (SCNA) | SCNA_input.txt | SCNA_output.txt |
| Methylation | DNAmethylation_input.csv | DNAmethylation_output.csv |
| Reverse Phase Protein Array (RPPA) | RPPA_input.csv | RPPA_output.csv |
| Mutated Pathways | mutatedpath_input.tsv | mutatedpath_output.tsv |
All supplemental data (including tables, figures, and data files) for this publication are available in the Sage Bionetworks Synapse repository (doi:10.7303/syn2468297).
Tools for Exploring Data and Analyses
- Next Generation Clustered Heatmaps, MD Anderson Cancer Center
- UCSC Cancer Genomics Browser, University of California, Santa Cruz
- Gitools, UPF-Barcelona
Associated Data Files
The analyses were derived from a data freeze for 12 TCGA cancer types made on December 22, 2012. The sample lists for the data freeze are available in the Sage Bionetworks Synapse repository (doi:10.7303/syn300013).
Instructions for Data Download
Open Access Data
- Download the appropriate manifest file from the publication page
- Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
- GDC DTT (Download, User's Guide)
- GDC API (User’s Guide)
Controlled Access Data
- Download the appropriate manifest file from the publication page
- Download a token from the GDC Data Portal
- GDC Data Portal (Launch, User’s Guide)
- Use the manifest file and token to download data using the GDC DTT or the GDC API
- GDC DTT (Download, User’s Guide)
- GDC API (User’s Guide)
For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.