bMSI-CAST: a systematic method for next generation sequencing-based microsatellite instability detection in plasma cell-free DNA

Abstract

Microsatellite instability (MSI) is a phenotypic manifestation of mismatch repair (MMR) deficiency and has been used as a biomarker through NGS-based assays to aid clinical cancer diagnosis and prognosis, as being advantageous over traditional electrophoresis-based tests and immunohistochemistry. Critical to detection accuracy but seldomly systematically discussed and poorly resolved by currently available methods are topics such as influences of changing experimental conditions, MSI-specific duplication removal and tradeoffs associated with loci selection strategies. In seeking solution to these questions, we have developed b/tMSI-CAST (blood/tissue MSI Caller Adjusted with Sequence duplicaTes), an integrated method consisting of a set of loci selection principles, an MSI-specific duplication removal strategy and a two-mode calling algorithm targeting both blood and tissue samples, equipped with a baseline construction method based on duplication distributions. We benchmarked b/tMSI-CAST against two established tools, mSINGS and MSIsensor-pro and found b/tMSI-CAST showed matched performance as MSIsensor-pro and outperformed mSINGS. We further applied it to a retrospective cohort of 18084 clinical samples to present a comprehensive landscape view on MSI prevalence across 26 cancer types, the largest of its kind in Chinese population so far, and demonstrated it on presurgical cfDNA samples of patients with early stage cancers.