alias: "NCI_22 WXS - Tumor, tumors in prostate"
title: "Tumor WXS in patients with small cell cancer, tumors in prostate": Sample NCI_22
design: "Formalin-fixed, paraffin-embedded (FFPE) tumor tissue samples were prepared. One hundred nanograms of DNA was sheared to approximately 200 base pairs (bp) by sonication (Covaris, Woburn, MA). Exome enrichment was performed using SureSelect Clinical Research Exome Kits according to the  manufacturer's instructions (Agilent, Santa Clara, CA). Paired-end sequencing (2 x 75 bp) was performed on an Illumina NextSeq500 instrument. The sequences were compared to the human reference genome hg19 using internally developed ClinOmics somatic Bioinformatic Pipeline v3.1. ANNOVAR was used to functionally annotate genetic variants. Variants with variant allele frequency (VAF) > 0.10, tumor sequencing depth > 50, and matched germline sequencing depth > 50 were considered. FACETS algorithm was used to determine total and allele-specific DNA copy number from WXS."
identifiers.namespace: NIH-phs002327
identifiers.id: "NCI_22 WXS - Tumor, tumors in prostate"
attributes.tag: alignment_software
attributes.value: ClinOmics somatic Bioinformatic Pipeline v3.1