TCGA Ovarian Serous Cystadenocarcinoma (OV)

Overview

The TCGA ovarian serous cystadenocarcinoma study — canonical cBioPortal studyId ov_tcga — is the landmark multi-platform genomic characterization of high-grade serous ovarian cancer (HGSOC) conducted by The Cancer Genome Atlas Research Network. SNV and CNA calls are publicly available via cBioPortal and from Synapse (syn11801889 for mutational signature data). Reference genome: hg19. PMID:35764743

Composition

  • Cancer type: HGSOC, predominantly stage III/IV.
  • 148 TCGA-OV patients contributed to the Boehm et al. 2022 multimodal HGSOC cohort (296 MSKCC + 148 TCGA-OV, total N=444). PMID:35764743
  • TCGA-OV cases used for CNA and SNV calls downloaded from cBioPortal, plus SBS3 frequencies from Synapse (syn11801889). HRD/HRP classification applied to TCGA cases using these calls. PMID:35764743

Assays / panels (linked)

  • Whole-exome sequencing, RNA-seq, copy-number alteration profiling (multi-platform).

Papers using this cohort

  • PMID:35764743 — Boehm et al. 2022, Nature Cancer: 148 TCGA-OV patients (stage III/IV HGSOC) integrated with 296 MSKCC cases in a multimodal late-fusion prognostic model combining CT radiomics, H&E histopathology, and genomics.

Notable findings derived from this cohort

  • CNA and SNV calls from TCGA-OV cBioPortal + SBS3 frequencies from Synapse were used to assign HRD/HRP/ambiguous status; combined with MSKCC MSK-IMPACT HRD calls, training split was 119 HRD / 218 HRP / 67 ambiguous. PMID:35764743
  • Availability of only CT imaging (not H&E WSIs or clinical sequencing) for all TCGA-OV cases constrained the full multimodal integrator; adding clinical features including RD-status and PARP-inhibitor annotation was not possible for TCGA-OV cases. PMID:35764743

Sources

  • cBioPortal study: https://www.cbioportal.org/study/summary?id=ov_tcga
  • PMID:35764743 — Boehm et al. 2022, Nature Cancer.

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