Cancer Cell. Volume 31 Issue 2: p181-193, 13 February 2017 10.1016/j.ccell.2017.01.001
We report a comprehensive molecular characterization of pheochromocytomas and paragangliomas (PCCs/PGLs), a rare tumor type. Multi-platform integration revealed that PCCs/PGLs are driven by diverse alterations affecting multiple genes and pathways. Pathogenic germline mutations occurred in eight PCC/PGL susceptibility genes. We identified CSDE1 as a somatically mutated driver gene, complementing four known drivers (HRAS, RET, EPAS1, and NF1). We also discovered fusion genes in PCCs/PGLs, involving MAML3, BRAF, NGFR, and NF1. Integrated analysis classified PCCs/PGLs into four molecularly defined groups: a kinase signaling subtype, a pseudohypoxia subtype, a Wnt-altered subtype, driven by MAML3 and CSDE1, and a cortical admixture subtype. Correlates of metastatic PCCs/PGLs included the MAML3 fusion gene. This integrated molecular characterization provides a comprehensive foundation for developing PCC/PGL precision medicine.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (21 Files)
- Controlled-Access Data - Download Manifest (3 Files)
Supplemental Data
- MAF Files
- Open-Access MAFs - PR_TCGA_PCPG_PAIR_Capture_All_Pairs.aggregated.capture.tcga.uuid.curated.somatic.maf
- Controlled-Access MAFs - TCGA_PCPG_PAIR.combined.annotated.last_freeze.maf
- Full Disease Sample List
- PCPG DCC Data Freeze - PCPG.freeze.2016.02.28.txt
- SNP and Copy Number variation from Affymetrix SNP6
- Level 1 Data Archives - broad.mit.edu_PCPG.Genome_Wide_SNP_6.Level_1.366.2006.0.tar.gz
- Level 2 Data Archives - broad.mit.edu_PCPG.Genome_Wide_SNP_6.Level_2.366.2006.0.tar.gz
- Level 3 Data Archives - broad.mit.edu_PCPG.Genome_Wide_SNP_6.Level_3.366.2006.0.tar.gz
- Mage-tab Data Archive - broad.mit.edu_PCPG.Genome_Wide_SNP_6.mage-tab.1.2006.0.tar.gz
- RNA Expression from IlluminaHiseq RNASeqV2
- Level 3 Data Archives - unc.edu_PCPG.IlluminaHiSeq_RNASeqV2.Level_3.1.2.0.tar.gz
- Mage-tab Data Archive - unc.edu_PCPG.IlluminaHiSeq_RNASeqV2.mage-tab.1.2.0.tar.gz
- miRNA from IlluminaGA
- Level 3 Data Archives - bcgsc.ca_PCPG.IlluminaHiSeq_miRNASeq.Level_3.1.1.0.tar.gz
- Mage-tab Data Archive - bcgsc.ca_PCPG.IlluminaHiSeq_miRNASeq.mage-tab.1.2.0.tar.gz
- Methylation from Illumina Infinium Human Methylation450
- Level 1 Data Archives - jhu-usc.edu_PCPG.HumanMethylation450.Level_1.1.0.0.tar.gz
- Level 2 Data Archives - jhu-usc.edu_PCPG.HumanMethylation450.Level_2.1.0.0.tar.gz
- Level 3 Data Archives - jhu-usc.edu_PCPG.HumanMethylation450.Level_3.1.0.0.tar.gz
- Mage-tab Data Archive - jhu-usc.edu_PCPG.HumanMethylation450.mage-tab.1.0.0.tar.gz
- Reverse Phase Protein Array (RPPA) Expression
- Level 1 Data Archives - mdanderson.org_PCPG.MDA_RPPA_Core.Level_1.1.0.0.tar.gz
- Level 2 Data Archives - mdanderson.org_PCPG.MDA_RPPA_Core.Level_2.1.0.0.tar.gz
- Level 3 Data Archives - mdanderson.org_PCPG.MDA_RPPA_Core.Level_3.1.0.0.tar.gz
- Mage-tab Data Archive - mdanderson.org_PCPG.MDA_RPPA_Core.mage-tab.1.0.0.tar.gz
- Other Data Files
- Methylation data - PCPG_methData_n178_20150708.txt.zip
- miRNA expression - PCPG.miRNAseq.RPM.1212maturestrands.miRBaseV16.hg19.n173freeze.txt.zip
- mRNA expression (log2 transformed) - PCPG_mRNA_expression_naRM.log2.csv.zip
- RPPA pathway scores - PCPGpathwayscores_6.8.15.csv.zip
- RPPA expression data - PCPG_RPPA.csv.zip
Additional Resources
- TCGA Analytical Tools (link is external) TCGA
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.