The Somatic Genomic Landscape Of Chromophobe Renal Cell Carcinoma

Cancer Cell. Volume 26: 319-330, 21 August 2014 10.1016/g.ccr.2014.07.014

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.

Data in the GDC

• GDC Manifests
  • Open-Access Data - Download Manifest (16 Files)
  • Controlled-Access Data - Download Manifest (6 Files)

Supplemental Data

These data represent a data freeze from Sept 06, 2013.

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

• Full KICH Sample List
  • KICH_Final_Data_Freeze_SampleList [txt]
  • KICH_Final_Data_Freeze [txt]
    The data freeze list with the following headers: PATIENT_BARCODE, SAMPLE_BARCODE, ALIQUOT_BARCODE, ALIQUOT_UUID, DATATYPE, PLATFORM_NAME, FILE_LOCATION_URL, DATA_LEVEL, ARCHIVE_NAME, BATCH_NUMBER, DATE_ADDED, SAMPLE ANNOTATIONS
• IlluminaGA: Wig, VCF and MAF files:
  • BAM Freeze List [tsv]
  • Whole exome DNA sequencing
    • Open Access Mutation Data
      • KICH.Broad.IlluminaGA_DNASeq.Public_Mutations [tar.gz]
      • KICH.Baylor.IlluminaGA_DNASeq.Public_Mutations [tar.gz]
    • Controlled Access Mutation Data
      • KICH.Broad.IlluminaGA_DNASeq_Cont.Protected_Mutations [tar.gz]
      • KICH.UCSC.IlluminaGA_DNASeq_Cont.Protected_Mutations [tar.gz]
        
      • KICH.Baylor.IlluminaGA_DNASeq_Cont.Protected_Mutations [tar.gz]
        
  • Whole genome DNA sequencing - KICH.wgs.maf
• RNA Expression from IlluminaHiseq RNASeqV2
  • Level 3 Data Archives - KICH.RNASeqV2.Level_3 [tar.gz]
  • mage-tab Archives - KICH.RNASeqV2.mage-tab [tar.gz]
• SNP and Copy Number variation from Affymetrix SNP6
  • Level 3 Data Archives - KICH.Genome_Wide_SNP_6.Level_3 [tar.gz]
  • Level 2 Data Archives - KICH.Genome_Wide_SNP_6.Level_2 [tar.gz] KICH.UCSC.IlluminaGA_DNASeq_Cont.Protected_Mutations [tar.gz]
    
  • Level 1 Data Archives - KICH.Genome_Wide_SNP_6.Level_1 [tar.gz] KICH.UCSC.IlluminaGA_DNASeq_Cont.Protected_Mutations [tar.gz]
    
  • mage-tab Archives - KICH.Genome_Wide_SNP_6.mage-tab [tar.gz]
• miRNA from Illumina HiSeq 2000
  • Level 3 Data Archives - KICH.miRNASeq.Level_3 [tar.gz]
  • mage-tab Archives - KICH.miRNASeq.mage-tab [tar.gz]
• Methylation from Illumina Infinium Human Methylation450 and HumanMethylation27
  • Level 3 Data Archives - KICH.HumanMethylation450.Level_3 [tar.gz]
  • Level 2 Data Archives - KICH.HumanMethylation450.Level_2 [tar.gz]
  • Level 1 Data Archives - KICH.HumanMethylation450.Level_1 [tar.gz]
  • mage-tab Archives - KICH.HumanMethylation450.mage-tab.tar.gz [tar.gz]
• Clinical
  • KICH.Clinical [tar.gz] - XML files containing biospecimen processing and clinical data

Additional Resources

• GDC Encyclopedia
• Descriptions of TCGA data are provided in the TCGA Barcode Encyclopedia Page
• Genomic Data Commons Portal