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Georgiadis, Andrew; Durham, Jennifer N; Keefer, Laurel A; Bartlett, Bjarne R; Zielonka, Magdalena; Murphy, Derek; White, James R; Lu, Steve; Verner, Ellen L; Ruan, Finey; Riley, David; Anders, Robert A; Gedvilaite, Erika; Angiuoli, Sam; Jones, Siân; Velculescu, Victor E; Le, Dung T; Diaz, Jr, Luis A; Sausen, Mark
Clinical cancer research, 12/2019, Volume: 25, Issue: 23Journal Article
Microsatellite instability (MSI) and high tumor mutation burden (TMB-High) are promising pan-tumor biomarkers used to select patients for treatment with immune checkpoint blockade; however, real-time sequencing of unresectable or metastatic solid tumors is often challenging. We report a noninvasive approach for detection of MSI and TMB-High in the circulation of patients. We developed an approach that utilized a hybrid-capture-based 98-kb pan-cancer gene panel, including targeted microsatellite regions. A multifactorial error correction method and a novel peak-finding algorithm were established to identify rare MSI frameshift alleles in cell-free DNA (cfDNA). Through analysis of cfDNA derived from a combination of healthy donors and patients with metastatic cancer, the error correction and peak-finding approaches produced a specificity of >99% ( = 163) and sensitivities of 78% ( = 23) and 67% ( = 15), respectively, for MSI and TMB-High. For patients treated with PD-1 blockade, we demonstrated that MSI and TMB-High in pretreatment plasma predicted progression-free survival (hazard ratios: 0.21 and 0.23, = 0.001 and 0.003, respectively). In addition, we analyzed cfDNA from longitudinally collected plasma samples obtained during therapy to identify patients who achieved durable response to PD-1 blockade. These analyses demonstrate the feasibility of noninvasive pan-cancer screening and monitoring of patients who exhibit MSI or TMB-High and have a high likelihood of responding to immune checkpoint blockade. .
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