Background: Next-generation sequencing (NGS) of cancer gene panels are widely applied to enable personalized\ncancer therapy and to identify novel oncogenic mutations.\nMethods: We performed targeted NGS on 932 clinical cases of non-small-cell lung cancers (NSCLCs) using the Ion\nAmpliSeqââ??¢ Cancer Hotspot panel v2 assay.\nResults: Actionable mutations were identified in 65% of the cases with available targeted therapeutic options,\nincluding 26% of the patients with mutations in National Comprehensive Cancer Network (NCCN) guideline genes.\nMost notably, we discovered JAK2 p.V617F somatic mutation, a hallmark of myeloproliferative neoplasms, in 1% (9/\n932) of the NSCLCs. Analysis of cancer cell line pharmacogenomic data showed that a high level of JAK2 expression\nin a panel of NSCLC cell lines is correlated with increased sensitivity to a selective JAK2 inhibitor. Further analysis of\nTCGA genomic data revealed JAK2 gain or loss due to genetic alterations in NSCLC clinical samples are associated\nwith significantly elevated or reduced PD-L1 expression, suggesting that the activating JAK2 p.V617F mutation\ncould confer sensitivity to both JAK inhibitors and anti-PD1 immunotherapy. We also detected JAK3 germline\nactivating mutations in 6.7% (62/932) of the patients who may benefit from anti-PD1 treatment, in light of recent\nfindings that JAK3 mutations upregulate PD-L1 expression.\nConclusion: Taken together, this study demonstrated the clinical utility of targeted NGS with a focused hotspot\ncancer gene panel in NSCLCs and identified activating mutations in JAK2 and JAK3 with clinical implications inferred\nthrough integrative analysis of cancer genetic, genomic, and pharmacogenomic data. The potential of JAK2 and\nJAK3 mutations as response markers for the targeted therapy against JAK kinases or anti-PD1 immunotherapy\nwarrants further investigation.
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