Nature. 497: p67-73. 02 May 2013 10.1038/nature12113
We performed an integrated genomic, transcriptomic, and proteomic characterization of 373 endometrial carcinomas using array- and sequencing-based technologies. Uterine serous tumors and ~25% of high-grade endometrioid tumors have extensive copy number alterations, few DNA methylation changes, low ER/PR levels, and frequent TP53 mutations. Most endometrioid tumors have few copy number alterations or TP53 mutations but frequent mutations in PTEN, CTNNB1, PIK3CA, ARID1A, KRAS and novel mutations in the SWI/SNF gene ARID5B. A subset of endometrioid tumors we identified had a dramatically increased transversion mutation frequency, and newly identified hotspot mutations in POLE. Our results classified endometrial cancers into four categories: POLE ultramutated, microsatellite instability hypermutated, copy number low, and copy number high. Uterine serous carcinomas share genomic features with ovarian serous and basal-like breast carcinomas. We demonstrated that the genomic features of endometrial carcinomas permit a reclassification that may impact postsurgical adjuvant treatment for women with aggressive tumors.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (21 Files)
- Controlled-Access Data - Download Manifest (1 File)
Supplemental Data
- Sample Lists - below are links to cumulative list of samples for the publication
- Cumulative Sample List [txt] (13 KB) - Sample barcode list
- Cumulative Data Freeze List [txt.zip] (1 MB) - The data freeze list with the following headers: PATIENT_BARCODE, SAMPLE_BARCODE, ALIQUOT_BARCODE, ALIQUOT_UUID, DATATYPE, PLATFORM_NAME, FILE_LOCATION_URL, DATA_LEVEL, ARCHIVE_NAME, BATCH_NUMBER, and DATE_ADDED.
- Mutations - below are links to archives containing the supplementary data used in the analysis of mutation data and to archives containing MAF files with exome-based somatic mutations
- UCEC Somatic Mutations [zip] (7.3 MB)
- genome.wustl.edu_UCEC.IlluminaGA_DNASeq.Level_2.1.5.0.tar.gz [tar.gz] (9.8 MB) - MAF file from Washington University
- Expression
- Agilent microarray data [tar] (3.3. GB) - Levels 1-3 microarray expression data
- RNASeq [tar] (5.6 GB) - Level 3 RNA-seq expression data
- Copy Number
- broad.mit.edu_UCEC.Genome_Wide_SNP_6.Level_3.tar [tar] (18 MB) - a collection of Level 3 archives derived from Affymetrix SNP 6 platform
- hms.harvard.edu_UCEC.IlluminaHiSeq_DNASeqC.Level_3.2.1.0.tar.gz [tar.gz] (447 KB) - a collection of Level 3 archives containing both copy number and structural aberrations derived from low-pass whole-genome sequencing using the Illumina HiSeq platform
- GISTIC marker file [txt.zip] (13 MB)
- miRNA - below is a link to the Level 3 archive that contains miRNA data and analysis
- bcgsc.ca_UCEC.Illumina_miRNASeq.tar [tar] (27 MB)
- Methylation - below is a link to a file that contains Methylation data and analysis
- jhu-usc.edu_UCEC.HumanMethylation.Level_3.tar [tar] (2.8 GB) - Level 3 methylation data
- jhu-usc.edu_UCEC.HumanMethylation.Level_1-2.tar [tar] (2.8 GB) - Level 1-2 methylation data
- BAM File References: Updated May 6, 2014 to include CGHub submissions
- UCEC_Freeze_20120404_update.txt [csv/txt] (11 MB)
- Clinical - below are links to supplemental clinical data for the publication.
- Key Clinical Data [xls|tsv] (161 KB)
- nationwidechildrens.org_UCEC.bio.Level_1.tar [tar] (2.7 MB) - XML files containing biospecimen processing and clinical data
- Reverse Phase Protein Array (RPPA) Expression
- TCGA_UCEC_185Samples_RPPA_DATA_submitted.csv [csv] (379 KB) - TCGA UCEC RPPA data used for the manuscript. This data set contains 185 samples and 170 antibodies (proteins). These data have been normalized using Dr. Akbani’s z-normalization method
- mdanderson.org_UCEC.MDA_RPPA_Core.Level_1.1.0.0.tar.gz [tar.gz] (954 MB) - Level 1 RPPA data
- mdanderson.org_UCEC.MDA_RPPA_Core.Level_2.1.0.0.tar.gz [tar.gz] (299 KB) - Level 2 RPPA data
- mdanderson.org_UCEC.MDA_RPPA_Core.Level_3.1.0.0.tar.gz [tar.gz] (374 KB) - Level 3 RPPA data
- mdanderson.org_UCEC.MDA_RPPA_Core.mage-tab.1.0.0.tar.gz [tar.gz] (3.9 MB) - MAGE-TAB for RPPA data
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Controlled Access Data
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- GDC DTT (Download, User’s Guide)
- GDC API (User’s Guide)
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