Prostate Adenocarcinoma (TCGA, 2015)

Overview

TCGA multi-platform genomic characterization of prostate adenocarcinoma, representing one of the foundational reference datasets for prostate cancer genomics. Used as a comparator in studies of prostate cancer PDX models and FGFR1 expression patterns. PMID:38488813

Composition

  • 499 prostate adenocarcinoma (PRAD) patients; multi-platform TCGA profiling. PMID:38488813
  • Used as cross-reference validation for promoter CpG methylation–expression correlations of FGFR1 and other prostate cancer driver genes. PMID:38488813

Assays / panels (linked)

  • Whole-exome sequencing, RNA-seq, DNA methylation arrays, copy-number analysis. PMID:38488813

Papers using this cohort

  • PMID:38488813 — Integrative Molecular Analyses of the MD Anderson Prostate Cancer Patient-derived Xenograft (MDA PCa PDX) Series.
  • PMID:26855148 — Beltran et al. 2016, Nature Medicine: queried for NEPC classifier validation (n=460 treatment-naïve adenocarcinomas scored NEPC-high at 0%).
  • PMID:26928463 — Kumar et al., Nat Genet 2016: queried to verify metastasis-private mutations from prad_fhcrc rapid-autopsy cohort are non-driver.

Notable findings derived from this cohort

  • FGFR1 promoter CpG methylation inversely correlated with FGFR1 expression in both PDXs and TCGA-PRAD, confirming epigenetic regulation of FGFR1 in prostate cancer. PMID:38488813
  • Queried for the NEPC classifier validation (n=460 treatment-naïve adenocarcinomas); 0% scored NEPC-high, confirming the classifier’s specificity for castration-resistant neuroendocrine disease PMID:26855148
  • Used alongside prad_su2c_2015 to validate that metastasis-private mutations found at autopsy in the prad_fhcrc cohort are unlikely to be drivers (only 2/51 occurred at >5% frequency in these cohorts) PMID:26928463
  • Used for TRMT10A expression analysis vs normal prostate (n=52 normal, n=500 tumor), tumor-stage stratification, HR-gene Spearman correlations, and TRMT10A amplification/deletion frequencies (1.22–5.26% across mCRPC cohorts) PMID:28068672
  • Cited as a comparison primary-prostate-cancer cohort in the MSK-IMPACT prostate study; MSK locoregional tumors showed higher TP53 and FOXA1 frequencies than TCGA primaries PMID:28825054.
  • Used to validate NOL10 overexpression in tumor vs. normal prostate, allele-specific BCR and survival outcomes (rs4519489 A/A genotype HR=13.05 for OS, P=0.038), and correlation of elevated NOL10 with advanced T stage (P=0.0058), lymph-node metastasis (P=0.045), and Gleason score (P=0.015) PMID:28927585.

Sources

  • cBioPortal study prad_tcga PMID:38488813.
  • PMID:26855148 — Beltran et al. 2016, Nature Medicine: NEPC classifier validation using this cohort (n=460 treatment-naïve adenocarcinomas).

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