Microsatellite instability is a clinically actionable genomic indication for cancer immunotherapy. In microsatellite instability-high (MSI-H) tumors, defects in DNA mismatch repair (MMR) can cause a hypermutated phenotype where alterations accumulate in the repetitive microsatellite regions of DNA. MSI detection is typically performed by subjecting tumor tissue (“solid biopsy”) to clinical next-generation sequencing or specific assays, such as MMR IHC or MSI PCR. Circulating cell-free tumor DNA (cfDNA) testing (“liquid biopsy”) is rapidly emerging as a less invasive method for cancer detection and monitoring disease progression. Here, we explore the possibility of detecting MSI in cfDNA and develop a novel cfDNA MSI detection assay with high specificity.

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