Mutalyzer 2: next generation HGVS nomenclature checker

Bioinformatics, vol. 37, pp. 2811–2817

Abstract

MOTIVATION: Unambiguous variant descriptions are of utmost importance in clinical genetic diagnostics, scientific literature and genetic databases. The Human Genome Variation Society (HGVS) publishes a comprehensive set of guidelines on how variants should be correctly and unambiguously described. We present the implementation of the Mutalyzer 2 tool suite, designed to automatically apply the HGVS guidelines so users do not have to deal with the HGVS intricacies explicitly to check and correct their variant descriptions. RESULTS: Mutalyzer is profusely used by the community, having processed over 133 million descriptions since its launch. Over a five year period, Mutalyzer reported a correct input in ∼50% of cases. In 41% of the cases either a syntactic or semantic error was identified and for ∼7% of cases, Mutalyzer was able to automatically correct the description. AVAILABILITY AND IMPLEMENTATION: Mutalyzer is an Open Source project under the GNU Affero General Public License. The source code is available on GitHub (https://github.com/mutalyzer/mutalyzer) and a running instance is available at: https://mutalyzer.nl.

Authors 5

1. Jonathan K. Vis Aachen Department of Clinical Genetics Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Clinical Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

   Department of Human Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

2. Martijn Vermaat Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

3. Johan T. den Dunnen Aachen Department of Clinical Genetics Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Clinical Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

   Department of Human Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

4. Peter E.M. Taschner Aachen Department of Human Genetics Generade Centre of Expertise Genomics and Leiden Centre for Applied Bioscience

   University of Applied Sciences Leiden · Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

   Generade Centre of Expertise Genomics and Leiden Centre for Applied Bioscience, University of Applied Sciences Leiden , Leiden, The Netherlands

5. Jeroen F. J. Laros Aachen Department of Clinical Genetics Department of Human Genetics

   Leiden University Medical Center · National Institute for Public Health and the Environment

   Affiliation as printed

   Department of Clinical Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

   Department of Human Genetics, Leiden University Medical Center (LUMC) Leiden, The Netherlands

   National Institute for Public Health and the Environment (RIVM) , Bthoven, The Netherlands