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MIAmS: microsatellite instability detection on NGS amplicons data

Abstract : MOTIVATION: 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.
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https://hal.umontpellier.fr/hal-02549949
Contributeur : Nathalie Salvy-Cordoba <>
Soumis le : mardi 21 avril 2020 - 18:43:17
Dernière modification le : vendredi 15 mai 2020 - 12:22:10

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Frédéric Escudie, Charles van Goethem, David Grand, Julie Vendrell, Anna Vigier, et al.. MIAmS: microsatellite instability detection on NGS amplicons data. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz797⟩. ⟨hal-02549949⟩

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