TCGA Ovarian Serous Cystadenocarcinoma

Overview

Comprehensive genomic characterization of 489 clinically annotated high-grade serous ovarian carcinoma (HGSOC) samples from The Cancer Genome Atlas (TCGA). All patients had stage II-IV disease and received platinum-based chemotherapy (94% also received a taxane). The study integrated whole-exome sequencing (316 tumors with matched normals), DNA copy number profiling (all 489 samples via Affymetrix SNP6 arrays and Agilent arrays), mRNA expression from three platforms, miRNA expression, and Illumina 27K methylation arrays, making it one of the most comprehensive multi-platform genomic studies of ovarian cancer.

Composition

  • Cancer type: HGSOC
  • 489 stage II-IV HGSOC tumors; all received platinum-based chemotherapy; 94% received a taxane
  • WES: 316 tumors with matched normals (~180,000 exons, ~18,500 genes)
  • Copy number: all 489 samples via affymetrix-snp6 and Agilent arrays
  • mRNA expression from Agilent, Affymetrix HuEx, and Affymetrix U133A platforms
  • Illumina 27K methylation arrays; miRNA expression
  • Key clinical fields: stage, grade, overall survival, platinum response, BRCA status

Assays / panels (linked)

  • whole-exome-seq — 316 tumor/normal pairs, ~18,500 genes
  • affymetrix-snp6 — DNA copy number profiling in all 489 samples
  • gistic — focal copy number analysis identifying 113 significant aberrations

Papers using this cohort

  • PMID:21720365 — TCGA 2011, integrated genomic analysis of ovarian carcinoma

Notable findings derived from this cohort

  • TP53 mutated in 303/316 (96%) of sequenced HGSOC samples; only 9 genes significantly mutated above background PMID:21720365
  • BRCA1 germline mutations in 9%, somatic in 3%, and promoter methylation in 11.5% of cases; BRCA2 germline 8%, somatic 3% PMID:21720365
  • Homologous recombination defects present in ~50% of tumors (BRCA1/2 mutation, BRCA1 methylation, PTEN deletion, EMSY amplification, RAD51C methylation, ATM/ATR mutation, Fanconi anemia gene mutation) PMID:21720365
  • 113 significant focal DNA copy number aberrations; most common focal amplifications: CCNE1, MYC, MECOM (each >20% of tumors) PMID:21720365
  • Four transcriptional subtypes identified: Immunoreactive, Differentiated, Proliferative, Mesenchymal PMID:21720365
  • FOXM1 transcription factor network activated in 87% of cases; RB1 pathway deregulated in 67%; PI3K/RAS in 45% PMID:21720365
  • CCNE1 amplification mutually exclusive with BRCA inactivation (FDR-adjusted P = 0.0048) PMID:21720365
  • HR defects in ~50% of tumors provide rationale for olaparib PARP inhibitor therapy beyond germline BRCA carriers PMID:21720365

Sources

  • PMID:21720365 — TCGA Research Network, “Integrated genomic analyses of ovarian carcinoma,” Nature 2011
  • cBioPortal: https://www.cbioportal.org/study/summary?id=ov_tcga_pub

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