Targeted Cancer Exome Sequencing

Genomic DNA from each sample was sheared by the Covaris S220 (Covaris, MA, USA) and used for the construction of a library using CancerSCAN probes and the SureSelectXT reagent kit (HSQ; Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol. CancerSCAN was designed to enrich the exons of 83 genes, covering 366.2 kb of the human genome (Supplementary Table S1)^{41 (link)}. After enriched exon libraries were multiplexed, the libraries were sequenced on a HiSeq. 2500 sequencing platform (Illumina, San Diego, CA, USA). Briefly, a paired-end DNA sequencing library was prepared through gDNA shearing, end-repair, A-tailing, paired-end adaptor ligation, and amplification. After hybridization of the library with bait sequences for 27 h, the captured library was purified and amplified with an index barcode tag, and the library quality and quantity were measured. Sequencing of the exome library was performed using the 100 bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina).