The Somatic Genomic Landscape of Glioblastoma

Cell. Volume 155: p462-477, 10 October 2013 10.1016/j.cell.2013.09.034

We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.

Data in the GDC

• GDC Manifests
  • Open-Access Data - Download Manifest (61 Files)

Supplemental Data

These data represent a data freeze from Oct 10, 2012.

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.

• ceRNAs and target genes.docx
• Expression_signatures.xlsx
• Exome_Sequencing.xlsx
• Genomic_Rearrangements.xlsx
• miRNA-mRNA-network.xls
• Molecular_features_of_long-term-survivors.xlsx
• Molecular_subtype_classification.xlsx
• Pathways_enriched_in_GBM_gene_ceRNAs.xlsx
• RPPA signaling module scores per sample.xlsx

• Sample Lists - below are links to cumulative list of samples for the population
  Full GBM Sample List
  After the data freeze for this paper, several blood normal samples were found to be mistakenly labelled as tissue normals. The table below lists the aliquots from this publication that were affected. The GBM sequence data list has been revised, and the original with incorrect barcodes can be found here. Note that the BAM file names for these samples contains the original, incorrect, barcode.

  Incorrect Barcode	Correct Barcode
  TCGA-19-5958-11A-01D-1696-08	TCGA-19-5958-10A-01D-1696-08
  TCGA-19-5951-11A-01D-1696-08	TCGA-19-5951-10A-01D-1696-08
  TCGA-19-5955-11A-01D-1696-08	TCGA-19-5955-10A-01D-1696-08
  TCGA-19-5960-11A-01D-1696-08	TCGA-19-5960-10A-01D-1696-08
  TCGA-19-5959-11A-01D-1696-08	TCGA-19-5959-10A-01D-1696-08
  TCGA-19-5954-11A-01D-1696-08	TCGA-19-5954-10A-01D-1696-08
  TCGA-19-5952-11A-01D-1696-08	TCGA-19-5952-10A-01D-1696-08
  TCGA-19-5950-11A-01D-1696-08	TCGA-19-5950-10A-01D-1696-08
  TCGA-19-5947-11A-01D-1696-08	TCGA-19-5947-10A-01D-1696-08

  • GBM data freeze list (tab-delimited text format) (53M)
  • GBM sequence data list (tab-delimited text format)(184K)
• Copy Number Tables
  • TCGA_GBM_PCT_CNA_Annotation.txt
  • TCGA_GBM_PCT_CNA_Physical_triplet.txt
  • TCGA_GBM_PCT_CNA_Summary.txt
• Mutations
  • TCGA_GBM_PCT_hg19_combined_snp_indel.maf.pct
  • TCGA_GBM_PCT_hg19_combined_snp_indel_description.txt
• Open access MAF file
  • broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.100.1.0.tar.gz
  • broad.mit.edu_GBM.IlluminaGA_DNASeq.Level_2.100.1.0.tar.gz.md5
• Gene Expression
  • Level 3 Data Archives
    • GBM.Gene_Expression.Level_3.tar (79M)
    • GBM.Gene_Expression.Level_3.tar.md5
  • Level 2 Data Archives
    • GBM.Gene_Expression.Level_2.tar (133M)
    • GBM.Gene_Expression.Level_2.tar.md5
  • Level 1 Data Archives
    • GBM.Gene_Expression.Level_1.tar (1.4G)
    • GBM.Gene_Expression.Level_1.tar.md5
• SNP
  • Level 3 Data Archives
    • GBM.SNP.Level_3.tar (20M)
    • GBM.SNP.Level_3.tar.md5
• miRNA Expression
  • Level 3 Data Archives - unc.edu_GBM.H-miRNA_8x15K.Level_3.1.8.0.tar.gz (2.9M)
  • Level 2 Data Archives - unc.edu_GBM.H-miRNA_8x15K.Level_2.1.8.0.tar.gz (8.1M)
  • Level 1 Data Archives - unc.edu_GBM.H-miRNA_8x15K.Level_1.1.8.0.tar.gz (776M)
• Methylation
  • Methylation Summary Information
    • TCGA_GBM_dnameth_calls_20120112_ver3.txt
    • TCGA_GBM_dnameth_scores_20120112_ver3.txt
    • DNA.methylation.k6.txt
    • TCGA_GBM_dnameth_call_categories.txt
  • Level 3 Data Archives
    • GBM.HumanMethylation27.Level_3.tar (177M)
    • GBM.HumanMethylation27.Level_3.tar.md5
    • GBM.HumanMethylation450.Level_3.tar (1.2G)
    • GBM.HumanMethylation450.Level_3.tar.md5
  • Level 2 Data Archives
    • GBM.HumanMethylation27.Level_2.tar (121M)
    • GBM.HumanMethylation27.Level_2.tar.md5
    • GBM.HumanMethylation450.Level_2.tar (1.2G)
    • GBM.HumanMethylation450.Level_2.tar.md5
    • GBM.HumanMethylation_OMA002_CPI.Level_2.tar (1.4M)
    • GBM.HumanMethylation_OMA002_CPI.Level_2.tar.md5
    • GBM.HumanMethylation_OMA003_CPI.Level_2.tar (1.3M)
    • GBM.HumanMethylation_OMA003_CPI.Level_2.tar.md5
  • Level 1 Data Archives
    • GBM.HumanMethylation27.Level_1.tar (219M)
    • GBM.HumanMethylation27.Level_1.tar.md5
    • GBM.HumanMethylation450.Level_1.tar (1.1G)
    • GBM.HumanMethylation450.Level_1.tar.md5
    • GBM.HumanMethylation_OMA002_CPI.Level_1.tar (5M)
    • GBM.HumanMethylation_OMA002_CPI.Level_1.tar.md5
    • GBM.HumanMethylation_OMA003_CPI.Level_1.tar (6.6M)
    • GBM.HumanMethylation_OMA003_CPI.Level_1.tar.md5
• Reverse Phase Protein Array (RPPA)
  • Level 3 Data Archives
    • mdanderson.org_GBM.MDA_RPPA_Core.Level_3.1.0.0.tar.gz (3.39M)
    • mdanderson.org_GBM.MDA_RPPA_Core.Level_3.1.0.0.tar.gz.md5
  • Level 2 Data Archives
    • mdanderson.org_GBM.MDA_RPPA_Core.Level_2.1.0.0.tar.gz (3.36M)
    • mdanderson.org_GBM.MDA_RPPA_Core.Level_2.1.0.0.tar.gz.md5
  • Level 1 Data Archives
    • mdanderson.org_GBM.MDA_RPPA_Core.Level_1.1.0.0.tar.gz (987M)
    • mdanderson.org_GBM.MDA_RPPA_Core.Level_1.1.0.0.tar.gz.md5
• Clinical
  • GBM.Clinical.tar (56M)
  • GBM.Clinical.tar.md5

Additional Resources

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