design: Formalin-fixed, paraffin-embedded (FFPE) tumor obtained during surgery was processed for Whole Exome Sequencing (WES) and RNA Sequencing (RNA-Seq) at Personalis Inc. (Menlo Park, CA, USA). Briefly, one section was hematoxylin and eosin (H&E) stained and annotated by a pathologist for tumor content. The H&E annotations were transferred to adjacent sections and macro-dissection was performed. Dual isolation of nucleic acids was performed utilizing the AllPrep DNA/RNA FFPE Tissue kit (Qiagen), followed by quality control (QC) of extracted nucleic acids using Agilent Tape Station for size distribution assessment and fluorometric method for quantification. Additionally, DNA from matched normal samples (PBMCs taken prior to treatment) was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen) and assessed by QC metrics. Next, exome capture was performed using SureSelect Clinical Research Exome v2 (SSCRv2) (Agilent), according to manufacturers recommendations. Additional supplementation with Personalis ACE proprietary target probes was performed to enhance coverage (Patwardhan et al. 2015). Briefly, manufacturer protocols were modified to adjust the average library insert length to approximately 250 bp and the use of the KAPA HiFi DNA Polymerase (Kapa Biosystems) and Stranded RNA Sequencing kit (Kapa Biosystems) for DNA and RNA sequencing, respectively. DNA was sequenced to an average depth of coverage of 300X across the 74.8 Mb NeXT assay genomic footprint for tumor samples and 150X for matched normal samples. RNA was sequenced to an average output of 100 million paired-end reads (total of 200 M reads). Reads that mapped to the preferred transcript of each gene were counted to measure expression levels for genes from each tumor sample. Raw strand-specific counts per gene were generated by the STAR aligner (Personalis).