Whole-exome seq of human: adult human tumour
The buffy samples and tumor biopsies were stored at -80 C. Tumor biopsies were frozen in the O.C.T. Compound (Fisher Scientific) and sectioned into 1.5mL tubes for DNA extraction. The tumor sites were confirmed by H&E staining. Genomic DNA (gDNA) was extracted from buffy and tumor samples with the DNeasy Blood & Tissue Kits (Qiagen). The whole-exome sequencing libraries were prepared with the SureSelect Low Input Target Enrichment System (Agilent) and sequenced pair-ended on Illumina HiSeq. The reads were filtered with Trim Galore!, and mapped with Bowtie2 (Langmead and Salzberg, 2012). The somatic mutations were called via Platypus (Rimmer et al., 2014) and VarScan2 (Koboldt et al., 2013), and then analyzed by R package VariantAnnotation (Obenchain et al., 2014).