TCGA Kidney Renal Clear Cell Carcinoma — Publication Cohort

Overview

The TCGA clear cell renal cell carcinoma (ccRCC; CCRCC) publication cohort, analyzed in the landmark TCGA Research Network paper (Nature 2013, PMID:23792563). This is the primary-analysis cohort referenced as kirc_tcga_pub in cBioPortal, distinct from the full deposited study (kirc_tcga). It encompasses 446 primary nephrectomy specimens with histologically confirmed ccRCC subjected to multi-platform molecular characterization. A “Core” subset of 372 samples had data across all platforms.

Composition

  • 446 primary nephrectomy specimens, histologically confirmed clear cell RCC (CCRCC); ≥60% tumor nuclei by pathology review (median 85%).
  • 372-sample “Core” set with data across all platforms; 446-sample “Extended” set with data on at least one platform.
  • Whole-exome sequencing on 417 tumors yielding 36,353 putative somatic mutations; whole-genome sequencing on 22 tumors for calibration (83% WES mutation call confirmation rate).
  • Copy number: Affymetrix SNP 6.0 arrays.
  • mRNA: RNA sequencing; miRNA: miRNA sequencing; DNA methylation: 450K Human Methylation arrays (n=224 for SETD2 analysis); protein: Reverse Phase Protein Arrays (RPPA).

Assays / panels (linked)

Papers using this cohort

  • PMID:23792563 — The Cancer Genome Atlas Research Network 2013, “Comprehensive molecular characterization of clear cell renal cell carcinoma,” Nature.

Notable findings derived from this cohort

  • 19 significantly mutated genes (q<0.1) identified; top 8 (q<0.00001): VHL, PBRM1, SETD2, KDM5C, PTEN, BAP1, MTOR, and TP53. Only BAP1 mutation correlated with worse survival PMID:23792563.
  • Chromosome 3p loss in 91% of samples, encompassing VHL, PBRM1, BAP1, and SETD2; 14q loss (including HIF1A) in 45%; 5q gain in 67% PMID:23792563.
  • PI3K/AKT/mTOR pathway altered in ~28% of tumors by MEMo mutual-exclusivity analysis; EGFR over-expressed and phosphorylated in the alteration module PMID:23792563.
  • SETD2 mutation associated with regional DNA hypomethylation at non-promoter CpG sites (n=2,557 differentially methylated loci; FDR=0.001) PMID:23792563.
  • Recurrent SFPQ-TFE3 fusion in 5 samples, all VHL wildtype with X(p11) rearrangements PMID:23792563.
  • Four mRNA subtypes (m1–m4) with differential survival: m1 enriched for PBRM1 mutations (39%); m3 for CDKN2A deletion and PTEN mutation; m4 for BAP1 and MTOR mutations PMID:23792563.
  • Metabolic shift toward Warburg phenotype (decreased AMPK/Krebs cycle, increased pentose phosphate pathway and fatty acid synthesis) correlated with worse survival; mRNA, miRNA, and protein signatures added prognostic power beyond clinical variables in multivariate Cox analysis PMID:23792563.

Sources

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