Nature. 474: p609-615, 30 June 2011 10.1038/nature10166
The Cancer Genome Atlas (TCGA) project has analyzed mRNA expression, miRNA expression, promoter methylation, and DNA copy number in 489 high-grade serous ovarian adenocarcinomas (HGS-OvCa) and the DNA sequences of exons from coding genes in 316 of these tumors. These results show that HGS-OvCa is characterized by TP53 mutations in almost all tumors (96%); low prevalence but statistically recurrent somatic mutations in 9 additional genes including NF1, BRCA1, BRCA2, RB1, and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three miRNA subtypes, four promoter methylation subtypes, a transcriptional signature associated with survival duration and shed new light on the impact on survival of tumors with BRCA1/2 and CCNE1 aberrations. Pathway analyses suggested that homologous recombination is defective in about half of tumors, and that Notch and FOXM1 signaling are involved in serous ovarian cancer pathophysiology.
Data in the GDC
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- Open-Access Data - Download Manifest (16 Files)
- Controlled-Access Data - Download Manifest (3 Files)
Supplemental Data
These data represent a data freeze from Feb 02, 2012.
Some archives listed for download below contain more sample data than was in the publication. The Supplementary Table 1 should be used as the key for sample identification for data in those archives.
- Ovarian Sample Lists - below are links to cumulative list of samples for the two sets of batches that were used for the Ovarian publication
- Mutations - below is a link to a ZIP archive containing the supplementary data used in the analysis of mutation data and to Level 3 MAF archives containing exome-based somatic mutations
- TCGA-OV-mutations [zip]
- BCM somatic OV mutations [tar.gz]
- BI somatic OV mutations [tar.gz]
- WashU somatic OV mutations [tar.gz]
- Unified Expression
- Copy Number - below is a link to a collection of Level 3 archives for the Agilent 1M platform
- MSKCC Agilent 1M Copy Number Variation [tgz]
- GISTIC marker file [txt.gz]
- miRNA - below is a link to the Level 3 archive that contains miRNA data and analysis
- Methylation - below is a link to a file that contains Methylation data and analysis
- Exome Sequence BAM File References
- OVpubBAMfileRefs.txt [csv/txt]
- OVpubBAMfileRefs.xls [xls]
- BAM references as HTML [html]
- Clinical - below are links to supplemental clinical data for the publication.
Additional Resources
- GDC Encyclopedia
- Descriptions of TCGA data are provided in the TCGA Barcode Encyclopedia Page
- Genomic Data Commons Portal
Instructions for Data Download
Open Access Data
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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
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