Biospecimens were screened from retrospective banks of Tissue Source Sites under appropriate IRB approvals for newly diagnosed GBM with minimal 80% tumor cell percentage. RNA and DNA extracted from qualified specimens were distributed to TCGA centers for analysis. Whole genome-amplified genomic DNA samples from tumors and normals were sequenced by the Sanger method. Mutations were called, verified using a second genotyping platform, and systematically analyzed to identify significantly mutated genes after correcting for the background mutation rate for nucleotide type and the sequence coverage of each gene. DNA copy number analyses were performed using the Agilent 244K, Affymetrix SNP6.0, and Illumina 550K DNA copy number platforms. Sample-specific and recurrent copy number changes were identified using various algorithms (GISTIC, GTS, RAE). mRNA and miRNA expression profiles were generated using Affymetrix U133A, Affymetrix Exon 1.0 ST, custom Agilent 244K, and Agilent miRNA array platforms. mRNA expression profiles were integrated into a single estimate of relative gene expression for each gene in each sample. Methylation at CpG dinucelotides was measured using the Illumina GoldenGate assay. All data for DNA sequence alterations, copy number, mRNA expression, miRNA expression, and CpG methylation were deposited in standard common formats in the TCGA DCC at http://cancergenome.nih.gov/dataportal/ . All archives submitted to DCC were validated to ensure a common document structure and to ensure proper use of identifying information.
Protocol detail
Comprehensive Genomic Profiling of Glioblastoma
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Assay
Cell
Dna sequence
Exon
Gene
Gene expression
Genome
Methylation
Mirna
Mrna
Mutations
Nucleotide
Tumor
Tumors dna
Corresponding Organization :
Other organizations : Duke University, Emory University, Henry Ford Health System, The University of Texas MD Anderson Cancer Center, University of California, San Francisco, Baylor College of Medicine, Harvard University Press, Massachusetts Institute of Technology, Washington University in St. Louis, University of Southern California, Johns Hopkins University, Ghent University Hospital, Ann Arbor Center for Independent Living, University of Michigan–Ann Arbor, Stanford University, Lawrence Berkeley National Laboratory, University of California, Berkeley, Walter and Eliza Hall Institute of Medical Research, Memorial Sloan Kettering Cancer Center, Cornell University, University of North Carolina at Chapel Hill, Translational Genomics Research Institute, National Institutes of Health
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Variable analysis
independent variables
- Tissue Source Sites
- Sample-specific and recurrent copy number changes identified using various algorithms (GISTIC, GTS, RAE)
- DNA sequence alterations, copy number, mRNA expression, miRNA expression, and CpG methylation data
- Newly diagnosed GBM with minimal 80% tumor cell percentage
- Mutations called and verified
- DNA copy number analyses
- MRNA and miRNA expression profiles
- Methylation at CpG dinucelotides
- Appropriate IRB approvals
- Qualified specimens
- Whole genome-amplified genomic DNA samples from tumors and normals
- Verified mutations using a second genotyping platform
- Correcting for the background mutation rate for nucleotide type and the sequence coverage of each gene
- Integrating mRNA expression profiles into a single estimate of relative gene expression for each gene in each sample
- Validating all archives submitted to DCC to ensure a common document structure and proper use of identifying information
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