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However, accurate quantification of MSI intensity is challenging due to the heterogeneous cellular composition of the tumor microenvironment. To this end, we introduce scMnT, a bioinformatic method for identifying MSI cells at single-cell resolution and quantifying MSI intensity based on microsatellite allele lengths. Applying scMnT to scRNA-seq datasets produced robust results and revealed substantial variation in MSI intensity among colorectal cancer patients, with higher MSI intensity correlating with improved responses to immunotherapy. Our approach provides a novel framework for analyzing MSI at the single-cell level, allowing new opportunities for MSI research. scMnT is publicly available at https:\/\/github.com\/18parkky\/scMnT.<\/jats:p>","DOI":"10.1093\/bib\/bbag156","type":"journal-article","created":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T12:42:19Z","timestamp":1774010539000},"source":"Crossref","is-referenced-by-count":0,"title":["Analysis of microsatellite instability intensity in single-cell resolution with scMnT reveals tumor heterogeneity in colorectal cancer"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-8821-7746","authenticated-orcid":false,"given":"Gyumin","family":"Park","sequence":"first","affiliation":[{"name":"School of Life Sciences, Gwangju Institute of Science and Technology (GIST) , Gwangju 61005 ,","place":["Republic of 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