{"owner":"TCGA","longTitle":"TCGA lung squamous cell carcinoma (LUSC) segmented copy number","cohort":"TCGA Lung Squamous Cell Carcinoma (LUSC)","url":"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lusc/cgcc/broad.mit.edu/genome_wide_snp_6/snp/","dataSubType":"copy number segments","security":"public","label":"Before remove germline cnv","tags":["cancer","non-small cell lung cancer"],"path":"data/public/TCGA/LUSC/SNP6_genomicSegment","anatomical_origin":["Lung"],"name":"TCGA.LUSC.sampleMap/SNP6_genomicSegment","dataproducer":"Broad Institute of MIT and Harvard University cancer genomic characterization center","wrangling_procedure":"Level_3 data download from TCGA DCC, processed at UCSC into cgData repository","sample_type":["tumor"],"assembly":"hg19","redistribution":true,"domain":"TCGA","type":"genomicSegment","wrangler":"cgData TCGAscript SNP6 processed on 2017-09-08","version":"2017-09-08","unit":"log2(tumor/normal)","primary_disease":"lung squamous cell carcinoma","platform":"SNP6","description":"TCGA lung squamous cell carcinoma (LUSC) segmented copy number variation profile.<br><br> Copy number profile was measured experimentally using the Affymetrix Genome-Wide Human SNP Array 6.0 platform at the Broad TCGA genome characterization center. Raw copy numbers were estimated at each of the SNP and copy-number markers. <a href=\"http://www.ncbi.nlm.nih.gov/pubmed/15475419\" target=\"_blank\"><u>Circular binary segmentation</u></a> was then used to segment the copy number data. Segments are mapped to hg19 genome assembly at Broad. Reference to the algorithm used by Broad to produce the dataset: <a href =\"https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/lusc/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_LUSC.Genome_Wide_SNP_6.mage-tab.1.2015.0/DESCRIPTION.txt\" target=\"_blank\"> <u>DCC description</u></a> and <a href=\"http://www.nature.com/nature/journal/vaop/ncurrent/suppinfo/nature07385.html\" target=\"_blank\"><u>nature 2008</u></a> .<br><br>"}