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. 2021 Sep 29;37(18):2811-2817.
doi: 10.1093/bioinformatics/btab051.

Mutalyzer 2: next generation HGVS nomenclature checker

Mihai Lefter  1 , Jonathan K Vis  1   2 , Martijn Vermaat  1 , Johan T den Dunnen  1   2 , Peter E M Taschner  1   3 , Jeroen F J Laros  1   2   4
Affiliations

Mutalyzer 2: next generation HGVS nomenclature checker

Mihai Lefter et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Elementary variants of descriptions NG_012337.1:g.[7G>T; 14del] (a) and NG_012337.1:g.[7G>T; 15del] (b) applied to a reference sequence in order to obtain the same observed sequence
Fig. 2.
Fig. 2.
Mutalyzer usage per tool and interface, extracted from https://mutalyzer.nl in December 2019
Fig. 3.
Fig. 3.
Assessments made by the Name Checker for all submitted descriptions
Fig. 4.
Fig. 4.
Common error codes returned by the Name Checker
Fig. 5.
Fig. 5.
Common warning codes issued by the Name Checker
Fig. 6.
Fig. 6.
Usage of reference sequence types
Fig. 7.
Fig. 7.
Reference genomes used in Position Converter descriptions
Fig. 8.
Fig. 8.
Example of different sequences between an NC and an NM
See this image and copyright information in PMC

References

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