WXS of prostatic stromal tumor
DNA was extracted from the tissue cores punched out from the selected areas of formalin-fixed paraffin-embedded specimens following QIAamp protocol (Qiagen, Foster City, CA). The quantity (OD 260 nm) and quality (OD 260 nm/OD 280 nm) of DNA in the obtained solution is measured using an ND-1000 spectrophotometer (Nanodrop Technology, Wilmington, DE). The integrity of the DNA is determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). We used Agilent SureSelect XT Reagent kit protocol for Illumina Hiseq paired-end sequencing library (catalog#G9611A). In all cases, the SureSelect XT Human All Exon Version 5 probe set was used. We constructed library with Agilent SureSelect XT Reagent kit. The amplification adapter-ligated sample was purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA) and analyzed on a Bioanalyzer DNA1000 chip. 500ng of the sample DNA was prepared for the hybridization with the capture baits, and the sample was hybridized for 24 hours at 65C, captured with the Dynabeads MyOne Streptavidin T1 (Life Technologie, USA) and purified using Agencourt AMPure XP beads. All samples were sequenced on Illumina HiSeq 2000.