Whole Genome Sequencing for Tumor Analysis

As orthogonal sequencing data for comparison, we conducted conventional WGS on the normal sample and metastatic tumor samples. Whole genome libraries for the normal and metastatic samples were prepared and sequenced with standard TruSeq protocols. The normal and left metastatic sample were sequenced at Illumina (San Diego, CA, USA) on an Illumina 2500 with 100 by 100-bp paired-end reads, and the right metastatic sample was sequenced at Macrogen (Seoul, South Korea) on a HiSeq X with 150 by 150-bp paired-end reads. Sequence reads were aligned to the human genome version GRCh37.1 using the BWA-MEM algorithm of the Burrows-Wheeler Aligner (BWA) v0.7.4 [23 (link)] with default parameters. Read mapping and sequencing coverage statistics are listed in Additional file 1: Table S2. The GATK (v3.3) DepthOfCoverage tool was used to calculate coverage metrics [24 (link)].