Whole Exome Sequencing of Tumor Samples

All tumor tissues were microscopically evaluated and assessed by a pathologist for tumor content. Genomic DNA was isolated from snap frozen tumor tissue and from matched blood prior to whole exome sequencing. Briefly, hybrid selection was performed with the Human All Exon kit SureSelect Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA) version 6 on the Illumina NovoSeq platform as paired-end 150-base pair reads. Alignment of read pairs were performed using Burrows-Wheeler Aligner (BWA MEM, http://bio-bwa.sourceforge.net/) to the human reference genome NCBI GRC Build 37 (hg19)^{30 (link)}. Using Picard (http://broadinstitute.github.io/picard/), we marked the optical duplicates prior to base score recalibration with GATK version 4.1.4 for post-alignment data processing^{31 (link)}. To identify somatic variants from the normal and tumor BAM files, we used Mutect2 followed by annotating and prioritizing using VEP^{32 (link)}.