Cell. Volume 171 Issue 3: p540–556.e25, 19 October 2017 10.1016/j.cell.2017.09.007
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival 'neuronal' subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, lncRNA, and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma-in-situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.
Data in the GDC
Supplemental Data
- GDC Manifests
- Open-Access Data - Download Manifest (6 Files)
- Controlled-Access Data - Download Manifest (1 File)
- MAF Files
- Protected MAF - broad.mit.edu_BLCA412.IlluminaGA_DNASeq.publication_version.protected.maf
- Data Files
- 19 Adjacent Tissue Normals - BLCA.19_tissue_normals.8167_lncRNAs.Ens82.FPKM.txt
- 405 Primary Tumours - BLCA.405_primary_tumours.8167_lncRNAs.Ens82.FPKM.txt
- Data Freeze - BLCA_freeze_with_normals.2017_09_19.xlsx
- S1. Master Patient Table - Table_S1.2017_08_05.xlsx
- S2. Supplemental Data Files - Table_S2.Supplemental_data.2017_08_08.xlsx
- S3. Microbe Analysis Results - Table_S3.Microbe_analysis.2017_06_22.xlsx
Additional Resources
- Broad Institute FireCloud (link is external) The Broad Institute
- cBioPortal for Cancer Genomics (link is external) Memorial Sloan-Kettering Cancer Center
- TCGA Batch Effects (link is external) MD Anderson Cancer Center
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.