Glioblastoma DNA Copy Number


Significant somatic chromosomal aberrations in glioblastoma (TCGA)

The following depicts statistically significant genome-wide DNA copy-number aberrations in human glioblastoma. Aberrations were identified with RAE on Agilent 244K data processed at MSKCC. Both significant genomic gains and losses (light and dark blue respectively) are included in genomic coordinates (chromosomes indicated at center, centromere in red, acrocentric arms in black) as are independently significant amplifications and homozygous deletions (red and green respectively). Selected candidate target genes are included, while the full set of regions of interest (ROI) are available below. Genes with correlated transcript levels are available as Supplementary Table 3 in the TCGA publications (submitted). The tumor and normal tissue samples used for the RAE analysis are available upon request.

Selected candidate target genes are included, while the full set of regions of interest (ROI) are available in this spreadsheet.

Click on the figure to open the PDF version.


The RAE GBM data is also available as gene-specific copy number calls (11 MB Text file). The file contains copy-number calls for all Gene isoforms (Refseq). Values: -2 = homozygous deletion; -1 = hemizygous deletion; 0 = neutral / no change; 1 = gain; 2 = high level amplification.

RAE reference:
Functional copy-number alterations in cancer. Taylor BS, Barretina J, Socci ND, DeCarolis P, Ladanyi M, Meyerson M, Singer S, Sander C. PLoS ONE. 2008 Sep 11;3(9):e3179.
[PubMed Abstract] [Full Text] [PDF]

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