TCGA adrenocortical carcinoma (ACC) somatic mutation (bcm curated)

{"longTitle":"TCGA adrenocortical carcinoma (ACC) gene-level nonsilent somatic mutation (broad curated)","cohort":"TCGA Adrenocortical Cancer (ACC)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/acc/gsc/broad.mit.edu/illuminaga_dnaseq_curated/mutations/","probeMap":"probeMap/hugo_gencode_good_hg19_V24lift37_probemap","dataSubType":"somatic non-silent mutation (gene-level)","security":"public","label":"broad curated","method":"MuTect","tags":["cancer"],"path":"data/public/TCGA/ACC/mutation_curated_broad_gene","anatomical_origin":["Adrenal gland"],"name":"TCGA.ACC.sampleMap/mutation_curated_broad_gene","dataproducer":"Broad Institute Genome Sequencing Center","wrangling_procedure":"Download .maf file from TCGA DCC, processed into gene by sample matrix at UCSC, stored in the UCSC Xena repository","sample_type":["tumor"],"redistribution":true,"type":"genomicMatrix","wrangler":"xena TCGAscript maf processed on 2018-01-10","version":"2018-01-10","gdata_tags":["Broad Institute Genome Sequencing Center"],"unit":"binary non-silent mutation","primary_disease":"adrenocortical cancer","platform":"IlluminaGA","description":"TCGA adrenocortical carcinoma (ACC) somatic mutation data.  Sequencing data are generated on a IlluminaGA system. The calls are generated at Broad Institute Genome Sequencing Center using the MuTect method. <br><br> Red (=1) indicates that a non-silent somatic mutation (nonsense, missense, frame-shif indels, splice site mutations, stop codon readthroughs, change of start codon, inframe indels) was identified in the protein coding region of a gene, or any mutation identified in a non-coding gene. White (=0) indicates that none of the above mutation calls were made in this gene for the specific sample.<br><br>"}

TCGA adrenocortical carcinoma (ACC) gene-level nonsilent somatic mutation (broad curated)

{"longTitle":"TCGA adrenocortical carcinoma (ACC) copy number gistic2 thresholded estimate","cohort":"TCGA Adrenocortical Cancer (ACC)","min":-2,"url":"http://gdac.broadinstitute.org/runs/analyses__2016_01_28/data/ACC/20160128/","dataSubType":"copy number (gene-level)","security":"public","label":"gistic2 thresholded","max":2,"tags":["cancer"],"path":"data/public/TCGA/ACC/Gistic2_CopyNumber_Gistic2_all_thresholded.by_genes","anatomical_origin":["Adrenal gland"],"name":"TCGA.ACC.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 adrenocortical cancer","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":"adrenocortical cancer","description":"TCGA adrenocortical carcinoma (ACC) 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>"}