| CPC G16B 25/10 (2019.02) [C12Q 1/6827 (2013.01); C12Q 1/6869 (2013.01); G16B 20/00 (2019.02); G16B 20/20 (2019.02); G16B 30/10 (2019.02); G16B 40/00 (2019.02); G16H 50/20 (2018.01); G16H 50/30 (2018.01); G01N 2570/00 (2013.01); Y02A 90/10 (2018.01)] | 7 Claims |
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1. A method of treating a cancer patient with immune therapy, comprising:
obtaining, from the cancer patient, a tumor sample and a matched normal sample;
obtaining omics data from the tumor sample and matched normal sample, wherein the omics data comprises whole genome and/or exome sequencing data, RNA sequencing data, and transcriptomics data;
comparing, in silico, the whole genome and/or exome sequence of the tumor sample with the matched normal sample to identify at least one of an APOBEC mutational signature and a POLE mutational signature, wherein the APOBEC signature is selected from the group consisting of: TpCpS→TpKpS, TpCpN→TpApN, and TpCpW→TpKpW, wherein S is C or G, K is G or T, N is C or G or A or T, and W is A or T, and/or wherein the POLE signature is selected from the group consisting of: TpCpT→TpApT and TpTpT→TpGpT;
comparing, in silico, the whole genome transcriptomics data of the tumor sample with the matched normal sample to quantify over-expression of a plurality of genes associated with checkpoint inhibition, wherein the genes associated with checkpoint inhibition are selected from the group consisting of: IDO, TDO, TIM3, CD40, LAG3, PD-L1, PD-L2, CTLA4, PD1, and IL2;
determine a positive microsatellite instability (MSI) status from the sequenced whole genome and/or exome; and
treating the cancer patient with immune therapy upon identifying APOBEC or POLE mutational signature, overexpression of the plurality of genes associated with checkpoint inhibition, and/or a positive MSI, wherein the immune therapy includes a checkpoint inhibitor.
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