Prostate Adenocarcinoma (TCGA, PanCancer Atlas 2018)

Overview

The TCGA Prostate Adenocarcinoma PanCancer Atlas 2018 cohort is the prostate cancer arm of the TCGA PanCancer Atlas, available in cBioPortal as prad_tcga_pan_can_atlas_2018. It covers prostate adenocarcinoma samples with uniformly reprocessed mutation calls (MC3 pipeline), copy-number profiles, and RNA-seq expression. Prostate cancer in TCGA is predominantly primary, treatment-naive disease; the meta-cohort prad_p1000 augments this with metastatic samples.

Composition

  • Cancer type: Prostate Adenocarcinoma (PRAD), OncoTree code PRAD.
  • Approximately 499 tumor samples.
  • Data modalities: WES, RNA-seq, SNP array.
  • Somatic mutations from MC3 ensemble pipeline.
  • Copy-number from Affymetrix SNP 6.0 / ABSOLUTE.

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • TMPRSS2-ERG is the most-recurrent intra-cancer fusion in the entire TCGA pan-cancer cohort, occurring in 38.2% of PRAD samples (205 samples); all 205 are flagged as harboring a druggable fusion per DEPO annotation, making PRAD the single largest contributor to the pan-cancer druggable-fusion count (6.0% of pan-cancer samples overall) PMID:29617662.
  • TMPRSS2-ERG fusions predicted a mean of approximately 1.5 fusion-derived neoantigens per fusion-bearing sample (range varies by specific breakpoint), with the majority being inframe fusions yielding fewer epitopes than frameshifts PMID:29617662.
  • In the pan-cancer analysis spanning this cohort, PRAD had a median of 1 fusion per sample (pan-cancer median), but the TMPRSS2-ERG fusion drives a strong enrichment of the ETS-family fusion subtype specific to prostate epithelium PMID:29617662.

Sources

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