Genomic DNA (30–200 ng) was fragmented to 200 bp using a Covaris E Series, and the resultant libraries were subjected to DNA Capture using a SureSelect XT Human All Exon v4 kit (Agilent) following the manufacturer’s instructions. Final libraries were quantified using qPCR and clustered at a molarity of 14.5 pmol/L, and sequencing was performed on an Illumina HiSeq 2000 using 2 × 75 cycles of version 3 SBS chemistry. Reads were aligned to the human reference genome (GRCh37) using Burrows-Wheeler Algorithm (v0.7.5a; ref. 22 (link)). PCR duplicates were filtered out from the subsequent analysis using Picard Tools (v1.94) and variants were called using the GATK pipeline (v2.3.9) best practices (23 (link)). Somatic changes among germline, cancer samples, and the PDX samples were investigated using MuTect (v1.1.4; ref. 24 (link)) and filtered for on-target regions using bedTools (v2.17.0). Comparisons between allele frequencies of somatic mutations in the cancer and PDX samples were investigated using R (3.1.2). All sequencing data have been deposited in the National Center for Biotechnology Information Sequence Read Archive under accession SRP072158.