Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion

By Johan T. den Dunnen, Stylianos E. Antonarakis. 2000

1,717 citations recorded by the source corpus.

Consistent gene mutation nomenclature is essential for efficient and accurate reporting, testing, and curation of the growing number of disease mutations and useful polymorphisms being discovered in the human genome. While a codified mutation nomenclature system for simple DNA lesions has now been adopted broadly by the medical genetics community, it is inherently difficult to represent complex mutations in a unified manner. In this article, suggestions are presented for reporting just such complex mutations. Hum Mutat 15:7–12, 2000. © 2000 Wiley‐Liss, Inc.

Subfields: Genetics

View Paper: https://www.semanticscholar.org/paper/8b7ca42c0ca9704b928a11e6865a5b6ffd27a878

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Citations in the corpus

• ClinVar: improving access to variant interpretations and supporting evidence (2017, background): “(iii) ClinVarVariationRelease represents Human Genome Variation Society (HGVS) (3) expressions for transcripts, and corresponding proteins, as a tuple with molecular consequence.”
• STrengthening the REporting of Genetic Association Studies (STREGA)— An Extension of the STROBE Statement (2009, neutral): “For variations not listed in dbSNP that can be described relative to a specified version, guidelines have been proposed [147,148].”
• ClinVar: public archive of interpretations of clinically relevant variants (2015, background): “Sequence variants submitted as Human Genome Variation Society (HGVS) expressions (6) are validated; once validated, HGVS expressions are calculated for a subset of other reference sequences that align to the variant’s location.”
• COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer (2009, neutral): “This mutation ‘syntax’ is derived from the HGVS nomenclature recommendations (3).”
• Oncotator: cancer variant annotation tool (2015, methodology): “Variant classification terms defined by the TCGA are used and nomenclature adheres to specifications defined by the Human Genome Variation Society (http://www.hgvs.org/mutnomen) (Dunnen et al., 2000).”
• The Ensembl Variant Effect Predictor (2016, methodology): “HGVS notations are also derived from TranscriptVariationAlleles, though they undergo significant additional processing to conform to the nomenclature definition (den Dunnen and Antonarakis 2000).”
• Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker (2008, background): “This problem was recognized several years ago, leading to proposals for nomenclature guidelines [Antonarakis et al., 1998], which were extended later [den Dunnen and Antonarakis, 2000].”
• The IPD and IMGT/HLA database: allele variant databases (2014, methodology): “The Human Genome Variation Society (HGVS) reporting system (14,15), is another method for reporting alleles.”
• De novo mutations in the sodium-channel gene SCN1A cause severe myoclonic epilepsy of infancy. (2001, methodology): “The SCN1A mutations were described according to the nomenclature established by den Dunnen and Antonarakis (2000), and numbering was started from the initiating ATG codon, as described by Escayg et al. (2000).”
• LOVD v.2.0: the next generation in gene variant databases (2011, methodology): “This tool performs an automatic check for compliance to the HGVS sequence variant nomenclature guidelines [Den Dunnen and Antonarakis, 2000; Den Dunnen and Paalman, 2003] to guarantee error-free entry of the sequence variants submitted.”
• Human Splicing Finder: an online bioinformatics tool to predict splicing signals (2009, background): “In order to easily study a group of mutations from different genes and transcripts, the mutation must be described by using the international nomenclature system for cDNA mutations (67) (http:// www.”