Academic journals are still a major conduit for the sharing of data on new scientific discoveries, and despite the continued rise in importance of electronic databases, they will continue to be so for some time to come. Numerous journals publish information about genetic variants and their effect on human health and well-being on an almost daily basis. To maximise the usefulness of this information and its translation into health care, the Human Variome Project believes that all sequence variants reported in journal articles should not only be fully and accurately described within the articles that report them, but also deposited into the appropriate gene/disease specific databases prior to publication.
We work with journal editors and publishers to adapt their existing editorial policies and author guidelines to ensure that authors check the sequence variant nomenclature that they use and submit their data to public databases, prior to submitting their manuscripts for publication.
The list below tracks journals in the life-sciences domain and whether or not they:
- mandate the use of correct sequence variant nomenclature, and
- require the submission of all sequence variants in a public database before publication.
If you notice an error or an omission in this list, please contact the International Coordinating Office.
Journals
Information for Journal Editors
Journal editors that wish to modify their author instructions are free to use and adapt the following example.
Gene symbols and OMIM numbers
All manuscripts must include HGNC-approved gene symbols (https://www.genenames.org/) and OMIM database reference numbers (https://www.omim.org/) for human genes and/or disorders. Gene symbols may be requested for loci for which no symbol exists using the Gene symbol request form (https://www.genenames.org/cgi-bin/request). In addition, commonly used alternative gene and disease symbols may also be used in the abstract and as key words. Note: OMIM entries now clearly indicate the current HGNC-approved gene symbol, but it may not be listed in the main title. In addition, there are separate OMIM numbers for diseases and genes and they are not to be used interchangeably.
Genome Sequence Variants
Because of the importance of the issue and the general consensus on the rules, <insert journal name> is adopting an editorial policy that requires absolute compliance with the rules to describe chromosomal and gene sequence variants before manuscripts will be accepted and published.
When referring to an alteration to the genome, the term "variant" is preferred to "mutation" (Cutting, 2014, Am J Hum Genet 4:5-10). "Mutation" may be used when referring to the process by which a new variant arises.
Acceptance and/or publication may be delayed if authors are unable to follow the guidelines properly.
Structural variants
Prior to publication, authors with articles describing structural and copy number variants (CNVs) are required to submit all such variants to either the Database of Genomic Variants Archive (DGVa; https://www.ebi.ac.uk/dgva/) or the Database of Genomic Structural Variation (dbVar) (https://www.ncbi.nlm.nih.gov/dbvar/). Genomic structural variation can be complex to represent, so authors should follow the guidance provided on the GDVa and dbVar sites. If the data include clinical assertions, they should be submitted to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/), not dbVar. The associated identification numbers should be used to describe the variants in the manuscript. A figure or table that encapsulates the full results of your genome-wide scan must be submitted as well.
Variants affecting individual genes
Authors must ensure that sequence variants in individual genes are correctly described and are deposited into the appropriate Locus Specific Database (LSDB) for the gene or disease of interest prior to acceptance and publication. Variants should be described in the text and tables using both DNA and protein designations whenever appropriate. Variants described only in the context of protein-sequence changes are not acceptable.
Requirements for variant descriptions
Reference sequences
Variants must be reported in the context of a defined reference sequence. Authors should always include the HGNC gene symbol and the GenBank Accession Number of the relevant reference sequence(s), with version number (e.g., RefSeq NM_123456.3 or GenBank U654321.1), in the Materials and Methods section and as a footnote in tables listing variants. Authors are encouraged to use the Locus Reference Genomic (LRG) reference sequence ( https://www.lrg-sequence.org/) which dispenses with the need for sequence versions, if a record exists for the gene in question (e.g., LRG_1).
Variant nomenclature
The most current guidelines are summarized on the Sequence Variation Nomenclature Homepage at the HGVS website (https://www.hgvs.org/mutnomen/). Examples of acceptable nomenclature are also provided. If alternative nomenclature schemes (e.g., for legacy exon or amino-acid numbering) are commonly found in the literature, they may also be used in addition to approved nomenclature, but they must be defined clearly. Variants may be described using dbSNP identifiers (e.g., rs123456:A>G). However, it is not acceptable to specify a gene symbol and variant description (e.g., COL1A1:c.572G>A) as this fails to specify a reference sequence.
Authors should also refer to den Dunnen and Antonarakis, 2000, Hum Mutat 15:7-12 and to den Dunnen and Paalman, 2003, Hum Mutat 22:181-182 for additional information.
Complex rearrangements can be described using the HGVS nomenclature (Taschner and den Dunnen, 2011, Hum Mutat 32:507-511) and the nomenclature is being adapted to accommodate the reporting of chromosomal variants detected by several technologies.
Chromosomal variants detected by karyotype analysis should be described using ISCN nomenclature for cytogenetic notation (see Shaffer, McGowan-Jordan and Schmid, eds. 2013. ISCN 2013: An International System for Human Cytogenetic Nomenclature [Basel: Karger]).
Variant checking
Authors are advised to check sequence variant descriptions using the Mutalyzer program (https://mutalyzer.nl/). Using batch mode, several variants can be analysed at once. Please see the article by Wildeman et al., 2008, Hum Mutat 29:6-13 for more information.
Submission of variants to databases
We support the recommendations of the Human Variome Project (Kohonen-Corish et al., 2010, Hum Mutat 31:1374-1381). Consequently, authors are required to submit all variants included in an article to a public database, preferably a gene variant database (LSDB), prior to acceptance.
Authors must confirm the status of database submission in their covering letter. In addition, authors should note in the manuscript (e.g., in the methods section) the database(s) to which they have submitted their variants and provide the URL(s). We encourage the use of widely accessible genetics databases as repositories for human gene sequence variation information. Links to gene variant databases can be obtained from the Human Variome Project web site (https://www.humanvariomeproject.org/resources/resources.html) or using the URL "GeneSymbol".lovd.nl (e.g. https://TP53.lovd.nl).
