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Study Description

The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies. Glioblastoma, the most common type of adult brain tumor, was the first cancer studied by TCGA. In this article, Comprehensive genomic characterization defines human glioblastoma genes and core pathways (The Cancer Genome Atlas Research Network, 2008; PMID: 18772890), tumors and matched-normal controls are used to identify aberrations in DNA copy number, sequence, methylation, and gene expression.

This dbGaP submission contains copy number variation and somatic single-nucleotide polymorphisms in 215 primary glioblastomas as well as clinical data. Other data in the article (The Cancer Genome Atlas Research Network, 2008) are not included in this submission but are available at the TCGA Data Portal, Comprehensive genomic characterization defines human glioblastoma genes and core pathways, http://tcga-data.nci.nih.gov/docs/publications/gbm_2008/.

Note: The Cancer Genome Atlas Research Network, 2008, refers to a total of 206 tumor and matched-control pairs. An additional nine (9) subjects were reported in MAF files in the Supplementary Data: TCGA-06-0142, TCGA-06-0150, TCGA-06-0151, TCGA-06-0159, TCGA-06-0160, TCGA-06-0165, TCGA-06-0167, TCGA-06-0216, TCGA-08-0245.

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Publicly Available Data (Public ftp)

Note: Access to publicly available data is available on the public ftp site for study phs000178.v6.p6.

Study Inclusion/Exclusion Criteria

Retrospective biospecimen repositories were screened for newly diagnosed glioblastoma based on surgical pathology reports and clinical records. Samples were further selected for having matched peripheral blood as well as associated demographic, clinical and pathological data. Corresponding frozen tissues were reviewed at the Biospecimen Core Resource (BCR) to ensure a minimum of 80% tumor nuclei and a maximum of 50% necrosis. DNA and RNA extracted from qualified biospecimens were subjected to additional quality control measurements before distribution to TCGA centers for analyses.

After exclusion based on insufficient tumor content (n = 234) and suboptimal nucleic acid quality or quantity (n = 147), 206 of the 587 biospecimens screened (35%) were qualified for copy number, expression and DNA methylation analyses. Of these, 143 cases had matched normal peripheral blood DNAs and were therefore appropriate for re-sequencing. This cohort also included 21 post-treatment glioblastoma cases used for exploratory comparisons. Although it is possible that a small number of progressive secondary glioblastomas were among the remaining 185 cases of newly diagnosed glioblastomas, this cohort represents predominantly primary glioblastoma.

Reprinted from The Cancer Genome Atlas Research Network, Nature. 2008 Oct 23;455(7216):1061-8, with permission from Nature Publishing Group.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Whole Genome Genotyping Affymetrix AFFY_6.0 934940 52074
Copy Number Analysis Agilent Human Genome CGH Microarray 244A N/A N/A
Whole Genome Genotyping Illumina HumanHap550v3.0 561466 51468
Study History

For an updated history of the program, please see:
http://cancergenome.nih.gov/abouttcga/overview/history

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