Cell. Volume 164: p550-563. 28 January 2016 10.1016/j.cell.2015.12.028
Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (43 Files)
- Controlled-Access Data - Download Manifest (1 Files)
Supplemental Data
- Methylation patient centric table
- Combined segmentation file
- HOMER motif
- Epigenetically Regulated Genes
- Methylation Signatures
- geneSelectedForClustering_Fig2B
These data represent a data freeze from Jan 5, 2015.
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.
- Full Disease Sample List
- AWG freeze list
- The DCC data freeze list with the following headers: PATIENT_BARCODE, SAMPLE_BARCODE, ALIQUOT_BARCODE, ALIQUOT_UUID, DATATYPE, PLATFORM_NAME, FILE_LOCATION_URL, DATA_LEVEL, ARCHIVE_NAME, BATCH_NUMBER, DATE_ADDED, SAMPLE ANNOTATIONS
- Exome Sequence BAM File References
Included in AWG freeze list (above) for the tabs WES (exome), WGS (whole genome) and WGA (amplified exome).
- Clinical - XML files containing biospecimen processing and clinical data
- Mutation
- AWG combined multicenter MAF (Not validated by DCC)
- DNA Copy Number
- GISTIC copy number matrix (1)
- GISTIC copy number matrix (2)
- Level 3 Data Archives :
- Mage-tab Data Archives :
- Full mRNA expression combined from microarray (Agilent) and RNA-seq (Illumina HiSeq RNASeq V2)
- RNA Expression from IlluminaHiseq RNASeqV2
- Gene expression matrix
- Level 3 Data Archives :
- GBM RNASeqV2 archive [1.5G]
- LGG RNASeqV2 archive [4.6G]
- Mage-tab Data Archives :
- Methylation from Illumina Infinium Human Methylation450 and Methylation27
- DNA methylation matrix
- Level 3 Data Archives:
- Level 2 Data Archives:
- Level 1 Data Archives:
- Mage-tab Archives:
- Protein Expression
- RPPA matrix
- Level 3 Data Archives:
- Level 2 Data Archives:
- Level 1 Data Archives:
- Mage-tab Archives:
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
- Download the appropriate manifest file from the publication page
- Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
- GDC DTT (Download, User's Guide)
- GDC API (User’s Guide)
Controlled Access Data
- Download the appropriate manifest file from the publication page
- Download a token from the GDC Data Portal
- GDC Data Portal (Launch, User’s Guide)
- Use the manifest file and token to download data using the GDC DTT or the GDC API
- GDC DTT (Download, User’s Guide)
- GDC API (User’s Guide)
For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.