{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,6]],"date-time":"2025-12-06T16:45:12Z","timestamp":1765039512047},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2019,10,24]],"date-time":"2019-10-24T00:00:00Z","timestamp":1571875200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Microsatellite instability (MSI) is a molecular marker of DNA mismatch repair deficiency frequently at play in oncogenesis. MSI testing is used for diagnostic, prognostic and therapeutic purposes in several cancers. The current gold standard analysis for microsatellite status is based on length distribution analysis of multiplex-PCR generated DNA fragments from tumor samples which is a laborious and time consuming method. Next generation sequencing (NGS) using amplicon panels is an easy, accurate and scalable technique to determine both the microsatellite status and tumor genome mutations at the same time. Here, we describe MIAmS, an application designed to tag microsatellite status from amplicon NGS of tumor samples. Interestingly, this tool does not require paired normal tissue for comparison. In addition, this scalable application provides a user-friendly report for the interpretation of the results by biologists and exhibits a strong accuracy and robustness for determination of the MSI status.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/bialimed\/miams. Evaluation data are available at http:\/\/www.ebi.ac.uk\/ena\/data\/view\/PRJEB31725.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz797","type":"journal-article","created":{"date-parts":[[2019,10,23]],"date-time":"2019-10-23T19:13:24Z","timestamp":1571858004000},"page":"1915-1916","source":"Crossref","is-referenced-by-count":11,"title":["MIAmS: microsatellite instability detection on NGS amplicons data"],"prefix":"10.1093","volume":"36","author":[{"given":"Fr\u00e9d\u00e9ric","family":"Escudi\u00e9","sequence":"first","affiliation":[{"name":"Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole , CHU Toulouse, France"}]},{"given":"Charles","family":"Van Goethem","sequence":"additional","affiliation":[{"name":"Department of Pathology and Oncobiology, Laboratoire de biologie des tumeurs solides, CHU de Montpellier, Univ. Montpellier , France"}]},{"given":"David","family":"Grand","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole , CHU Toulouse, France"}]},{"given":"Julie","family":"Vendrell","sequence":"additional","affiliation":[{"name":"Department of Pathology and Oncobiology, Laboratoire de biologie des tumeurs solides, CHU de Montpellier, Univ. Montpellier , France"}]},{"given":"Anna","family":"Vigier","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole , CHU Toulouse, France"}]},{"given":"Pierre","family":"Brousset","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole , CHU Toulouse, France"}]},{"given":"Sol\u00e8ne M","family":"Evrard","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole , CHU Toulouse, France"}]},{"given":"J\u00e9r\u00f4me","family":"Solassol","sequence":"additional","affiliation":[{"name":"Department of Pathology and Oncobiology, Laboratoire de biologie des tumeurs solides, CHU de Montpellier, Univ. Montpellier , France"}]},{"given":"Janick","family":"Selves","sequence":"additional","affiliation":[{"name":"Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole , CHU Toulouse, France"}]}],"member":"286","published-online":{"date-parts":[[2019,10,24]]},"reference":[{"key":"2023060911592522700_btz797-B1","author":"Gallon","year":"2018"},{"key":"2023060911592522700_btz797-B2","doi-asserted-by":"crossref","first-page":"e9393.","DOI":"10.1371\/journal.pone.0009393","article-title":"An optimized pentaplex PCR for detecting DNA mismatch repair-deficient colorectal cancers","volume":"5","author":"Goel","year":"2010","journal-title":"PLoS One"},{"key":"2023060911592522700_btz797-B3","doi-asserted-by":"crossref","first-page":"13321","DOI":"10.1038\/srep13321","article-title":"MSIseq: software for assessing microsatellite instability from catalogs of somatic mutations","volume":"5","author":"Huang","year":"2015","journal-title":"Sci. Rep"},{"key":"2023060911592522700_btz797-B4","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/bioinformatics\/btv589","article-title":"Jflow: a workflow management system for web applications","volume":"32","author":"Mariette","year":"2016","journal-title":"Bioinformatics"},{"key":"2023060911592522700_btz797-B5","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1093\/bioinformatics\/btt755","article-title":"MSIsensor: microsatellite instability detection using paired tumor-normal sequence data","volume":"30","author":"Niu","year":"2014","journal-title":"Bioinformatics"},{"key":"2023060911592522700_btz797-B6","first-page":"159","article-title":"Microsatellite instability in colorectal cancer","volume":"17","author":"Nojadeh","year":"2018","journal-title":"EXCLI J"},{"key":"2023060911592522700_btz797-B7","first-page":"2825","article-title":"Scikit-learn: machine learning in Python","volume":"12","author":"Pedregosa","year":"2011","journal-title":"J. Mach. Learn. 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