Genomic DNA was extracted using standard phenol–chloroform extraction methods. Whole-exome sequencing was performed to a mean depth of 292× with mean distinct coverage of 189× (Supplemental Table S1). Sequencing was performed by Personal Genome Diagnostics using methods previously described (Jones et al. 2015 ). Briefly, DNA was sheared using a Covaris sonicator and Illumina TruSeq library construction (Illumina) was performed using 50 ng to 3 µg of gDNA according to manufacturer's instructions. Exonic regions were captured using the Agilent SureSelect system (Agilent) per manufacturer's instructions. Paired-end sequencing was performed using HiSeq 2500 instrumentation (Illumina) to achieve sequencing of 100 bases from each end of the fragments. Analysis of somatic variants and copy-number alterations was performed by Personal Genome Diagnostics using methods previously described in detail (Jones et al. 2015 ). Somatic variants detected by these methods were further validated using MuTect (Cibulskis et al. 2013 (link)).