Sequencing of Cervical Cancer: Sample T7
Prior to library preparation, DNA was fragmented by sonication (Covaris, Woburn, MA) to 150 bp and purified using Agencourt AMPure XP beads. In brief, 50 ng of size‐selected DNA was then ligated to specific adaptors during library preparation (Illumina TruSeq, Illumina, San Diego, CA). Each library was made with sample‐specific barcodes, quantified by qPCR (Kapa Biosystems, Woburn, MA) and two libraries were pooled to a total of 500 ng for exome enrichment using the Agilent SureSelect hybrid capture kit (Whole Exome_v2, 44 Mb; Agilent Technologies, Santa Clara, CA). Several captures were pooled further and sequenced in one or more lanes to a final equivalent of two exomes per lane on a Hiseq 2000 (Illumina, San Diego, CA). Sequence demultiplexing, alignment, and recalibration were performed using BWA, PICARD, and GATK tools, as described previously.