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Describing structural changes by extending HGVS sequence variation nomenclature
Open accessAbstract
New technologies allow rapid discovery of novel sequence variants among which those involving complex structural rearrangements. The description of such complex variants challenges the existing standard sequence variation nomenclature of the Human Genome Variation Society (HGVS, http://www.hgvs.org/mutnomen), because this mainly focuses on simple variants. Here, we suggest several extensions of the HGVS nomenclature guidelines to facilitate unambiguous description of complex sequence variants at the DNA level. These include: (1) nesting to support description of changes within inversions and duplications, and (2) composite changes to support concatenation of inserted sequences. The advantage of these additions is that inversions and duplications with small differences and more complex variants can be described without reverting to the less informative indel description. In addition, they should provide sufficient flexibility and consistency, thereby limiting alternative interpretations and ambiguous descriptions. The specifications should allow easy implementation in sequence variant nomenclature checkers (e.g., Mutalyzer, http://www.mutalyzer.nl/). We are extending the functionality of Mutalyzer to incorporate the latest version of the HGVS sequence variation nomenclature guidelines.
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“Not all types of variants ( e.g. , complex variants) are covered by the HGVS recommendations, but possible descriptions for complex variants have been reported. 7,12”
From Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (2015) · cites this paper as [12]
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“, complex variants) are covered by the HGVS recommendations, but possible descriptions for complex variants have been reported.(7,12) In addition, this ACMG recommendation supports three specific exceptions to the HGVS nomenclature rules: 1) "X" is still considered acceptable for use in reporting nonsense variants in…”
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Metadata
- Authors
- Taschner, P. E. M., & den Dunnen, J. T.
- Affiliations
- Leiden University Medical Center (NL)
- Corresponding author
- Taschner, Peter E.M.
- Venue
- Human Mutation
- Publisher
- Hindawi Limited
- Published
- 2011-03-15
- Volume
- 32
- Issue
- 5
- Pages
- 507-511
- ISSN
- 1059-7794 (ISSN-L)
- OpenAlex
- W2112245868
- Cited by
- 61
- References
- 4
- Citations by year
- 2026: 1 · 2024: 1 · 2020: 3 · 2019: 2 · 2018: 6 · 2017: 8 · 2016: 8 · 2015: 11 · 2014: 10 · 2013: 4 · 2012: 4
- FWCI
- 4.20
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- HAL (submittedVersion, other-oa)
- Leiden Repository (Leiden University) (submittedVersion)
- Trinity's Access to Research Output (TARA) (Trinity College Dublin) (submittedVersion)
- Funders
- European Commission (200754)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- HGVS nomenclature, structural variants, inversion, duplication, nesting
- MeSH terms
- Base Sequence, Humans, Terminology as Topic, Software, Genetic Variation, Genome, Human, Guidelines as Topic, Internet
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