{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T17:17:09Z","timestamp":1784308629980,"version":"3.55.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR\u2013electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.<\/jats:p><jats:p>Availability and implementation: \u00a0https:\/\/github.com\/ding-lab\/msisensor<\/jats:p><jats:p>Contact: \u00a0kye@genome.wustl.edu or lding@genome.wustl.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt755","type":"journal-article","created":{"date-parts":[[2013,12,27]],"date-time":"2013-12-27T01:10:37Z","timestamp":1388106637000},"page":"1015-1016","source":"Crossref","is-referenced-by-count":750,"title":["MSIsensor: microsatellite instability detection using paired tumor-normal sequence data"],"prefix":"10.1093","volume":"30","author":[{"given":"Beifang","family":"Niu","sequence":"first","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Ye","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"},{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qunyuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"},{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Lu","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingchao","family":"Xie","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael D.","family":"McLellan","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael C.","family":"Wendl","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Ding","sequence":"additional","affiliation":[{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"},{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"},{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"},{"name":"1 Departments of Genetics and Mathematics, The Genome Institute, 2Department of Genetics, Division of Statistical Genomics, 3Department of Medicine and 4Siteman Cancer Center, Washington University in St. Louis, MO 63108, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2013,12,25]]},"reference":[{"key":"2023012710451336800_btt755-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc."},{"key":"2023012710451336800_btt755-B3","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/nature12113","article-title":"Integrated genomic characterization of endometrial carcinoma","volume":"497","author":"The Cancer Genome Atlas Research Network","year":"2013","journal-title":"Nature"},{"key":"2023012710451336800_btt755-B4","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1002\/(SICI)1097-0142(19980301)82:5<851::AID-CNCR8>3.0.CO;2-M","article-title":"Prognostic factors for patients with sarcomas of the pelvic bones","volume":"82","author":"Kawai","year":"1998","journal-title":"Cancer"},{"key":"2023012710451336800_btt755-B5","doi-asserted-by":"crossref","first-page":"e63056","DOI":"10.1371\/journal.pone.0063056","article-title":"A novel approach for characterizing microsatellite instability in cancer cells","volume":"8","author":"Lu","year":"2013","journal-title":"PLoS One"},{"key":"2023012710451336800_btt755-B6","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1126\/science.8066446","article-title":"MLH1, PMS1, and MSH2 interactions during the initiation of DNA mismatch repair in yeast","volume":"265","author":"Prolla","year":"1994","journal-title":"Science"},{"key":"2023012710451336800_btt755-B7","volume-title":"Biometry: The Principles and Practice of Statistics in Biological Research","author":"Sokal","year":"2012"},{"key":"2023012710451336800_btt755-B8","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1016\/S0016-5085(99)70510-X","article-title":"New clinical criteria for hereditary nonpolyposis colorectal cancer (HNPCC, Lynch syndrome) proposed by the International Collaborative group on HNPCC","volume":"116","author":"Vasen","year":"1999","journal-title":"Gastroenterology"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1015\/48921773\/bioinformatics_30_7_1015.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/7\/1015\/48921773\/bioinformatics_30_7_1015.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,22]],"date-time":"2024-05-22T04:52:18Z","timestamp":1716353538000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/7\/1015\/236553"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,12,25]]},"references-count":7,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2014,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt755","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,4,1]]},"published":{"date-parts":[[2013,12,25]]}}}