TCGA Chromophobe Renal Cell Carcinoma (2014)
Overview
TCGA multi-platform characterization of 66 primary chromophobe renal cell carcinomas (CHRCC) with matched normal tissue/blood collected from BWH, MSKCC, NCI, and MD Anderson. The study applied whole-exome sequencing, whole-genome sequencing (n=50), mtDNA sequencing (n=61), RNA-seq, miRNA-seq, HM450 methylation arrays, and Affymetrix SNP6 copy-number arrays. It is one of the TCGA pan-kidney analyses.
Composition
- 66 primary CHRCC tumors; histologic subtypes: classic (n=47), eosinophilic (n=19).
- Platforms: whole-exome-seq (NimbleGen VCRome 2.1 42 MB, 90% ≥20×), whole-genome-seq (n=50, 60×/30×), rna-seq, mirna-seq, hm450-methylation-array, affymetrix-snp6.
- Pipelines: Mercury alignment, gistic, mutsig, meerkat.
- Reference genome: hg19.
Assays / panels (linked)
Papers using this cohort
Notable findings derived from this cohort
- ChRCC has a low exonic mutation rate (~0.4/Mb); only TP53 (32%) and PTEN (9%) reached MutSig significance; 86% of cases showed characteristic loss of whole chromosomes 1, 2, 6, 10, 13, and 17 PMID:25155756.
- Recurrent genomic rearrangement breakpoints within ~10 kb upstream of the TERT TSS were found in 6/50 ChRCC by WGS, associated with >500-unit TERT expression — a novel TERT-upregulation mechanism distinct from C228T/C250T point mutations PMID:25155756.
- mTOR-pathway alterations (PTEN, MTOR, TSC1/TSC2, NRAS) spanned 23% of cases; elevated PPARGC1A and ~4× mitochondrial copy number indicate oxidative phosphorylation activation counter to the Warburg pattern of ccRCC PMID:25155756.
Sources
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