Targeted sequencing of 577 genes from 114 matched tumor and normal samples from 71 high-grade serous ovarian cancer (HGSC) participants and OncoScan somatic copy number analysis from 61 of the 71 HGSC participants.
The KAPA HyperPlus Kit (part number KK8514) was used to generate barcoded libraries from 500ng DNA according to the KAPA-provided protocol. Libraries were pooled and sequence capture was performed with custom NimbleGen SeqCap or Agilent SureSelectXT targeted-gene capture kits. The custom bait designs included 577 candidate cancer susceptibility genes involved in the response to DNA damage, DNA repair, cell cycle regulation, programmed cell death, and PI3K AKT mTOR pathways. The resulting post-capture enriched multiplexed sequencing libraries were sequenced with 2 × 100 bp paired end reads on a GAIIx or HiSeq 2500 using Illumina-provided protocols.