Verifying nomenclature of DNA variants in submitted manuscripts: Guidance for journals
Open accessAbstract
Documenting variation in our genomes is important for research and clinical care. Accuracy in the description of DNA variants is therefore essential. To address this issue, the Human Variome Project convened a committee to evaluate the feasibility of requiring authors to verify that all variants submitted for publication complied with a widely accepted standard for description. After a pilot study of two journals, the committee agreed that requiring authors to verify that variants complied with Human Genome Variation Society nomenclature is a reasonable step toward standardizing the worldwide inventory of human variation.
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The ABCD1 Variant Database reports all (likely) pathogenic and benign variants in conformity with the nomenclature recommended by the Human Genome Variation Society (HGVS).
“The ABCD1 Variant Database reports all (likely) pathogenic and benign variants in conformity with the nomenclature recommended by the Human Genome Variation Society (HGVS; https://varnomen.hgvs.org/) [20].”
From Structure and Function of the ABCD1 Variant Database: 20 Years, 940 Pathogenic Variants, and 3400 Cases of Adrenoleukodystrophy (2022) · cites this paper as [20]
The Recommended Guidelines section says variant descriptions should follow HGVS recommendations. Neither that section nor the passages retrieved for “ABCD1 Variant Database” and “pathogenic and benign variants” establishes that the ABCD1 Variant Database reports all such variants or that its entries conform to HGVS nomenclature. (LLM, conf=0.82)
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Research works printed but not linked: 9
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- den Dunnen JT (2016). Sequence variant descriptions: HGVS nomenclature and mutalyzer. Current Protocols in Human Genetics, 90(1), 7.13.1– 7.13.19. 10.1002/cphg.2 27367167 · DOI
- den Dunnen JT (2019). Efficient variant data preparation for Human Mutation manuscripts: Variants and phenotypes. Human Mutation, 40(8), 1009. 10.1002/humu.23830 31397982 · DOI
- den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, Mcgowan-Jordan J, Roux AF, Smith T, Antonarakis SE, & Taschner PEM (2016). HGVS recommendations for the description of sequence variants: 2016 update. Human Mutation, 37(6), 564– 569. 10.1002/humu.22981 26931183 · DOI
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- Landrum MJ, Chitipiralla S, Brown GR, Chen C, Gu B, Hart J, Hoffman D, Jang W, Kaur K, Liu C, Lyoshin V, Maddipatla Z, Maiti R, Mitchell J, O’Leary N, Riley GR, Shi W, Zhou G, Schneider V, … Kattman BL (2020). ClinVar: Improvements to accessing data. Nucleic Acids Research, 48(D1), D835– D844. 10.1093/nar/gkz972 31777943 PMC6943040 · DOI · Paper page
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Mallack, E. J., Gao, K., Engelen, M., & Kemp, S. (2022) · Cells · doi:10.3390/cells11020283 · Cited by 60 · see citing works
- Authors
- Higgins, J., Dalgleish, R., Dunnen, J. T., Barsh, G., Freeman, P. J., Cooper, D. N., Cullinan, S., Davies, K. E., Dorkins, H., Gong, L., Imoto, I., Klein, T. E., Korf, B., Misra, A., Paalman, M. H., Ratzel, S., Reichardt, J. K. V., Rehm, H. L., Tokunaga, K., Weck, K. E., & Cutting, G. R.
- Affiliations
- American College of Medical Genetics (US)
- University of Leicester (GB)
- Leiden University Medical Center (NL)
- HudsonAlpha Institute for Biotechnology Huntsville Alabama USA
- University of Manchester (GB)
- Cardiff University (GB)
- American Society of Human Genetics (US)
- University of Oxford (GB)
- University Hospitals of Leicester NHS Trust (GB)
- Stanford University (US)
- Aichi Cancer Center Research Institute (JP)
- University of Alabama at Birmingham (US)
- Public Library of Science (US)
- John Wiley & Sons (United States) (US)
- Australian Institute of Tropical Health and Medicine (AU)
- Broad Institute (US)
- National Center for Global Health and Medicine (JP)
- University of North Carolina at Chapel Hill (US)
- Johns Hopkins University (US)
- ORCID
- Venue
- Human Mutation
- Publisher
- Wiley
- Published
- 2020-12-10
- Volume
- 42
- Issue
- 1
- Pages
- 3-7
- ISSN
- 1059-7794 (ISSN-L)
- 1098-1004
- PMC
- PMC7961887
- OpenAlex
- W3110497308
- Cited by
- 13
- References
- 0
- Citations by year
- 2026: 1 · 2024: 4 · 2023: 2 · 2022: 1 · 2021: 5
- FWCI
- 7.46
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Human Mutation (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- PubMed Central (acceptedVersion)
- ResearchOnline at James Cook University (James Cook University) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Leiden Repository (Leiden University) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion, other-oa)
- Funders
- Japan Society for the Promotion of Science (18H02894)
- National Human Genome Research Institute (U41HG006834, U24HG010615)
- National Institute of General Medical Sciences (R24GM061374)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK044003)
- Topics
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Academic Writing and Publishing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Social Sciences › Decision Sciences › Information Systems and Management › Academic Publishing and Open Access
- Keywords
- Human Variome Project, journal editorial policy, human genetic variation
- MeSH terms
- DNA, Humans, Terminology as Topic, Periodicals as Topic, Pilot Projects, Publications, Genetic Variation, Genome, Human, Human Genome Project
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