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The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

Cancer Cell (2014), Volume xxx Number yyy, Published online 21 Aug. 2014, [doi:10.1016]

Abstract

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs), based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. Integrative analysis is consistent with ChRCC as originating from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicated changes in mitochondrial function as an inherent component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements led to recurrent structural breakpoints within TERT promoter region, which correlated with highly elevated TERT expression and manifestation of kataegis, representing a novel mechanism of TERT up-regulation in cancer, in addition to previously-observed amplifications and point mutations.

Associated Data Files

These data represent a data freeze from Sept 06, 2013. Please note that more recent data are available via the TCGA Data Portal.

The data are supported by different organizations. All data marked by [DCC] are DCC-validated archives. All data marked by [Supplementary] were created by the manuscript authors and you should contact the corresponding author for support.

Full KICH Sample List:

IlluminaGA: Wig, VCF and MAF files:

RNA Expression from IlluminaHiseq RNASeqV2

SNP and Copy Number variation from Affymetrix SNP6

miRNA from Illumina HiSeq 2000

Methylation from Illumina Infinium Human Methylation450 and HumanMethylation27

Clinical [DCC]

Additional Information