Sample processing and genomic profiling were performed in a Clinical Laboratory Improvement Amendments (CLIA)- and the College of American Pathologists (CAP)-accredited laboratory (Nanjing Geneseeq Technology Inc., Nanjing, China) as previously described [12 (link),13 (link)]. In brief, genomic DNA from tumor specimen and control samples were extracted and quantified by Qubit 3.0. Library preparations were performed with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Target enrichment was performed using customized xGen lockdown probes (Integrated DNA Technologies, Coralville, IA) targeting 474 cancer- and radiotherapy response-relevant genes (Radiotron gene panel, Nanjing Geneseeq Technology Inc.) (S2 Table). The hybridization capture reaction was performed with Dynabeads M-279 (Life Technologies, San Diego, CA) and xGen Lockdown hybridization and wash kit (Integrated DNA Technologies) according to manufacturer’s protocols. Captured libraries were on-beads polymerase chain reaction (PCR) amplified with Illumina p5 and p7 primers in KAPA HiFi HotStart ReadyMix (KAPA Biosystems), followed by purification using Agencourt AMPure XP beads. Libraries were quantified by quantitative real-time PCR using KAPA Library Quantification kit (KAPA Biosystems). Library fragment size was determined by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA).