TCGA pheochromocytoma and paraganglioma (PCPG) somatic mutation (ucsc automated)

{"cohort":"TCGA Pheochromocytoma & Paraganglioma (PCPG)","clinicalfeature":"TCGA.PCPG.sampleMap/PCPG_clinicalFeature","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/pcpg/bcr/","label":"Phenotypes","version":"2016-04-27","dataSubType":"phenotype","type":"clinicalMatrix","name":"TCGA.PCPG.sampleMap/PCPG_clinicalMatrix"}

{"longTitle":"TCGA pheochromocytoma and paraganglioma (PCPG) copy number gistic2 thresholded estimate","cohort":"TCGA Pheochromocytoma & Paraganglioma (PCPG)","min":-2,"url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/PCPG/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2 thresholded","max":2,"tags":["cancer"],"path":"data/public/TCGA/PCPG/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":["Paraganglia"],"name":"TCGA.PCPG.sampleMap/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","dataproducer":"TCGA FIREHOSE pipeline","wrangling_procedure":"FIREHOSE data download from TCGA DCC, processed at UCSC into xena repository","sample_type":["tumor"],"redistribution":true,"groupTitle":"TCGA pheochromocytoma & paraganglioma","type":"genomicMatrix","wrangler":"xena TCGAscript CopyNumber_Gistic2 processed on 2017-09-08","version":"2017-09-08","unit":"-2,-1,0,1,2: 2 copy del, 1 copy del, no change, amplification, high-amplification","primary_disease":"pheochromocytoma & paraganglioma","description":"TCGA pheochromocytoma and paraganglioma (PCPG) thresholded gene-level copy number variation (CNV) estimated using the GISTIC2 method.<br><br> Copy number profile was measured experimentally using whole genome microarray at a TCGA genome characterization center. Subsequently, GISTIC2 method was applied using the TCGA FIREHOSE pipeline to produce gene-level copy number estimates. GISTIC2 further thresholded the estimated values to -2,-1,0,1,2, representing homozygous deletion, single copy deletion, diploid normal copy, low-level copy number amplification, or high-level copy number amplification. Genes are mapped onto the human genome coordinates using UCSC xena HUGO probeMap. Reference to GISTIC2 method PMID:21527027.<br><br>"}