MIAmS: microsatellite instability detection on NGS amplicons data

Frédéric Escudié; Charles Van Goethem; David Grand; Julie Vendrell; Anna Vigier; Pierre Brousset; Solène M Evrard; Jérôme Solassol; Janick Selves

doi:10.1093/bioinformatics/btz797

MIAmS: microsatellite instability detection on NGS amplicons data

Bioinformatics. 2019 Oct 24:btz797. doi: 10.1093/bioinformatics/btz797. Online ahead of print.

Authors

Frédéric Escudié¹, Charles Van Goethem², David Grand¹, Julie Vendrell², Anna Vigier¹, Pierre Brousset¹, Solène M Evrard¹, Jérôme Solassol², Janick Selves¹

Affiliations

¹ Department of Pathology, Institut Universitaire du Cancer Toulouse Oncopole, CHU Toulouse, France.
² Department of Pathology and Oncobiology, Laboratoire de biologie des tumeurs solides, CHU de Montpellier, Univ. Montpellier, France.

PMID: 31647522
DOI: 10.1093/bioinformatics/btz797

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.

Availability: https://github.com/bialimed/miams.

Supplementary information: Supplementary data are available at Bioinformatics online, evaluation data are available at http://www.ebi.ac.uk/ena/data/view/PRJEB31725.