Cancer Cell. Volume 17: p98-110, 19 January 2010 10.1016/j.ccr.2009.12.020
The Cancer Genome Atlas Network recently catalogued recurrent genomic abnormalities in glioblastoma (GBM). We describe a robust gene expression-based molecular classification of GBM into Proneural, Neural, Classical and Mesenchymal subtypes and integrate multi-dimensional genomic data to establish patterns of somatic mutations and DNA copy number. Aberrations and gene expression of EGFR, NF1, and PDGFRA/IDH1 each define Classical, Mesenchymal, and Proneural, respectively. Gene signatures of normal brain cell types show a strong relation between subtypes and different neural lineages potentially indicative of distinct cell of origin. Additionally, response to aggressive therapy differed by subtype with greatest benefit in Classical and no benefit in Proneural. We provide a framework that unifies transcriptomic and genomic dimensions for GBM molecular stratification with important implications for future studies.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (21 Files)
Supplementary Files
- Individual platform gene level expression measurements for 202 samples
- Broad202.txt - Affymetrix-HT-HG-U133A GeneChip
- LBL202.txt - Affymetrix HuEx GeneChip
- UNC202.txt - Custom Agilent 244,000 feature Gene Expression Microarray
- Unified and integrated dataset created by combining the three individual sets using factor analysis
- unifiedScaled.txt - unified gene expression estimate for 202 samples and 11,861 genes
- unifiedScaledFiltered.txt - Filtered unified gene expression estimate for 202 samples and 1740 genes
- SAM_pairwise.xls - Rank-ordered Significance Analysis of Microarrays (SAM) lists for all pair wise comparisons [HTML]
- ROC_pairwise.xls - Rank-ordered ROC lists for all pair wise comparisons [HTML]
- ClaNC840_centroids.xls - ClaNC 840 gene list and centroids [HTML]
- TCGA_unified_CORE_ClaNC840.txt - Expression values and subtype calls for the Core TCGA samples using the unified scaled data
- Platform_Correlations.pdf - Spearman rank-order correlations of all three platforms
- Validation dataset combined from four public cohorts
The file CancerCell_GBM_validation.data.txt was posted on June 1, 2012 and supercedes Validation.txt
Additional Information
- exp2008_202SampleList.txt - A list of the 202 samples used for analysis in this publication
- IDH1-Mutated_Samples.txt - An updated list of IDH1 Mutated Samples (Nov 28, 2011) tab-delimited format
- IDH1-Mutated_Samples.xlsx - An updated list of IDH1 Mutated Samples (Nov 28, 2011) Excel format
- IDH1-Sample-Status.txt - An updated list of IDH1 Samples (Nov 28, 2011) tab-delimited format
- IDH1-Sample-Status.xlsx - An updated list of IDH1 Mutated Samples (Nov 28, 2011) Excel format
- Receptor_Tyrosine_Kinase_Gene_Expression_Data.zip - Receptor Tyrosine Kinase Gene Expression Data (using RT-PCR and Nanostring)
Additional Resources
- GDC Encyclopedia
- Descriptions of TCGA data are provided in the TCGA Barcode Encyclopedia Page
- Genomic Data Commons Portal
Instructions for Data Download
Open Access Data
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Controlled Access Data
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