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Techniques are rapidly evolving for the detection of MSI from tumor-normal paired or tumor-only sequencing data. However, tumor tissues are often insufficient, unavailable, or otherwise difficult to procure. Increasing clinical evidence indicates the enormous potential of plasma circulating cell-free DNA (cfNDA) technology as a noninvasive MSI detection approach. Results: We developed MSIsensor-ct, a bioinformatics tool based on a machine learning protocol, dedicated to detecting MSI status using cfDNA sequencing data with a potential stable MSIscore threshold of 20%. Evaluation of MSIsensor-ct on independent testing datasets with various levels of circulating tumor DNA (ctDNA) and sequencing depth showed 100% accuracy within the limit of detection (LOD) of 0.05% ctDNA content. MSIsensor-ct requires only BAM files as input, rendering it user-friendly and readily integrated into next generation sequencing (NGS) analysis pipelines. Availability: MSIsensor-ct is freely available at https:\/\/github.com\/niu-lab\/MSIsensor-ct. Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bib\/bbaa402","type":"journal-article","created":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T01:47:53Z","timestamp":1607564873000},"source":"Crossref","is-referenced-by-count":31,"title":["MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8871-4689","authenticated-orcid":false,"given":"Xinyin","family":"Han","sequence":"first","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"},{"name":"University of the Chinese Academy of Sciences, Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuying","family":"Zhang","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"},{"name":"University of the Chinese Academy of Sciences, Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel Cui","family":"Zhou","sequence":"additional","affiliation":[{"name":"McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA"},{"name":"Department of Medicine, Washington University in St. Louis, St. Louis, MO 63108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongliang","family":"Wang","sequence":"additional","affiliation":[{"name":"ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5481-2763","authenticated-orcid":false,"given":"Xiaoyu","family":"He","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"},{"name":"University of the Chinese Academy of Sciences, Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danyang","family":"Yuan","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"},{"name":"University of the Chinese Academy of Sciences, Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruilin","family":"Li","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiayin","family":"He","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaohong","family":"Duan","sequence":"additional","affiliation":[{"name":"ChosenMed Technology (Beijing) Co., Ltd., Beijing 100176, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael C","family":"Wendl","sequence":"additional","affiliation":[{"name":"McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA"},{"name":"Department of Genetics, Washington University in St. Louis, St. Louis, MO 63108, USA"},{"name":"Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63108, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Ding","sequence":"additional","affiliation":[{"name":"McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA"},{"name":"Department of Genetics, Washington University in St. Louis, St. Louis, MO 63108, USA"},{"name":"Department of Medicine, Washington University in St. Louis, St. Louis, MO 63108, USA"},{"name":"Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63108, 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