Broad Prostate Adenocarcinoma WES (prad_broad)

Overview

The Broad prostate adenocarcinoma WES dataset comprises 112 prostate adenocarcinoma/normal pairs from treatment-naive radical prostatectomy specimens sourced from American and Australian patients. Mean exome coverage was 118x (89.2% of targets at ≥20x). Copy-number profiling was performed on 169 tumors via Affymetrix SNP 6.0 arrays. RNA-seq was conducted on 22 exome-sequenced tumors and 41 independent samples. Additional validation cohorts covered >300 primary tumors and metastases from Weill Cornell Medical College, University of Michigan, Uropath, and University of Washington.

Composition

  • 112 prostate adenocarcinoma/normal pairs (radical prostatectomy, treatment-naive)
  • Cancer type: PRAD
  • 5,764 somatic mutations identified; median 30 non-silent mutations per tumor (~1.4 per Mb)
  • Copy-number profiling on 169 tumors (Affymetrix SNP 6.0)
  • RNA-seq on 22 exome-sequenced and 41 independent samples

Assays / panels (linked)

Papers using this cohort

Notable findings derived from this cohort

  • SPOP was the most frequently mutated gene at 13% (15/111 exomes); all mutations affect conserved residues in the substrate-binding cleft PMID:22610119
  • SPOP mutations and ETS rearrangements (TMPRSS2-ERG fusion) were mutually exclusive (P < 0.001, Fisher’s exact test) PMID:22610119
  • FOXA1 and MED12 identified as additional recurrent driver genes PMID:22610119
  • SPOP-mutant tumors enriched for 5q21 deletions (CHD1; P = 1.4e-11) and 6q21 deletions (FOXO3, PRDM1; P = 3.4e-7) PMID:22610119
  • 12 genes significantly enriched for mutations at q < 0.1 by MutSig analysis PMID:22610119

Sources

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