The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
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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Citations
Cites
International System for Human Cytogenetic Nomenclature
National Cancer Institute (2020) · Definitions · doi:10.32388/78qroa · Cited by 6,831
Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion
den Dunnen, J. T., & Antonarakis, S. E. (2000) · Human Mutation · doi:10.1002/(sici)1098-1004(200001)15:1 · Cited by 1,764
Wildeman, M., Ophuizen, E. A. A. V., den Dunnen, J. T., & Taschner, P. E. M. (2007) · Human Mutation · doi:10.1002/humu.20654 · Cited by 391
Self-citationPousi, B., Hautala, T., Hyland, J. C., Schröter, J., Eckes, B., Kivirikko, K. I., & Myllylä, R. (1998) · Human Mutation · doi:10.1002/(sici)1098-1004(1998)11:1 · Cited by 29
Cited by
Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., et al. (2015) · Genetics in Medicine · doi:10.1038/gim.2015.30 · Cited by 32,594
“, 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…”
MethodThe IPD and IMGT/HLA database: allele variant databases
Robinson, J., Halliwell, J. A., Hayhurst, J. D., Flicek, P., Parham, P., & Marsh, S. G. E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1161 · Cited by 1,732
College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests
Aziz, N., Zhao, Q., Bry, L., Driscoll, D. K., Funke, B., Gibson, J. S., Grody, W. W., Hegde, M., Hoeltge, G. A., Leonard, D. G. B., et al. (2014) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2014-0250-cp · Cited by 393
VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions
Freeman, P., Hart, R. K., Gretton, L. J., Brookes, A. J., & Dalgleish, R. W. M. (2017) · Human Mutation · doi:10.1002/humu.23348 · Cited by 201
Rubinstein, W. S., Maglott, D. R., Lee, J. M., Kattman, B. L., Malheiro, A. J., Ovetsky, M., Hem, V., Gorelenkov, V., Song, G., Wallin, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1173 · Cited by 185
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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