MSI expresso: a software for determining MSI status and detecting MSI-related transcription events from RNA sequencing data.

ABSTRACT: Microsatellite instability (MSI) is becoming increasingly important in oncology as it has been reported across more than two dozen of solid cancer types. The MSI-high phenotype has long been used as a predictive and prognostic marker in colorectal cancer and has been recently approved by the FDA as a marker for immune checkpoint blockade therapy for solid cancers. Several bioinformatics tools have been developed to assess MSI status of a tumor sample using Next-Generation Sequencing (NGS) data mostly from whole genome, whole exome, and targeted gene sequencing data. While most tools available only infer the MSI status, none of them use RNA-sequencing (RNA-seq) data and provide per microsatellite expression and genotype results. We present MSI Expresso, a software which assesses the MSI sta

SUBMITTER: Tubacher E 

PROVIDER: S-EPMC12058494 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature