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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

JournalNomenclatureSubmissionChecked
Advances in Genomics and Genetics  8/2016
American Journal of Human Genetics (AJHG)  5/2015
American Journal of Medical Genetics (AJMG) Part A  5/2015
American Journal of Medical Genetics (AJMG) Part B: Neuropsychiatric Genetics  5/2015
Annals of Human Genetics  5/2015
Annual Review of Genetics  5/2015
Annual Review of Genomics and Human Genetics  8/2016
Anticancer Research  5/2015
Antioxidants & Redox Signaling  5/2015
Arteriosclerosis, Thrombosis, and Vascular Biology  5/2015
Autism Research  5/2015
Balkan Journal of Medical Genetics  8/2016
BBA - Gene Regulatory Mechanisms  5/2015
Behavior Genetics  8/2016
Biochemical and Biophysical Research Communications (BBRC)  5/2015
Biochemical Genetics  8/2016
Biochemical Journal  10/2015
Biochemistry and Cell Biology  5/2015
Bioinformatics  5/2015
Biological Psychiatry  5/2015
Biology of Reproduction  5/2015
Birth Defects Research Part B: Developmental And Reproductive Toxicology  8/2016
Blood  5/2015
BMC Bioinformatics  8/2016
BMC Biology  8/2016
BMC Evolutionary Biology  8/2016
BMC Genetics  5/2015
BMC Genomics  8/2016
BMC Medical Genetics  8/2016
BMC Medical Genomics  8/2016
BMJ Case Reports  5/2015
Brain: A Journal of Neurology  5/2015
Briefings in Bioinformatics  5/2015
Briefings in Functional Genomics  8/2016
British Medical Journal (BMJ)  5/2015
Cancer Cell  5/2015
Cancer Gene Therapy  8/2016
Cancer Genetics  8/2016
Cancer Genomics & Proteomics  8/2016
Caryologia  8/2016
Cell  5/2015
Cell Research  5/2015
Cellular Reprogramming  8/2016
Chromosoma  8/2016
Chromosome Research  8/2016
Circulation: Cardiovascular Genetics  8/2016
Clinical Chemistry  5/2015
Clinical Dysmorphology  8/2016
Clinical Genetics  5/2015
Comparative Biochemistry and Physiology D: Genomics & Proteomics  8/2016
Comparative Cytogenetics  8/2016
Conservation Genetics  8/2016
Conservation Genetics Resources  8/2016
Critical Reviews In Eukaryotic Gene Expression  8/2016
Current Biology  5/2015
Current Gene Therapy  8/2016
Current Genetics  5/2015
Current Genomics  8/2016
Cytogenetic and Genome Research  5/2015
Development  5/2015
Development, Genes and Evolution  5/2015
Disease Markers  5/2015
DNA Repair  5/2015
Drugs of the Future  6/2015
Drugs of Today  6/2015
Endocrine-Related Cancer  6/2015
European Journal of Human Genetics  6/2015
European Journal of Medical Genetics  6/2015
Expert Reviews in Biomedicine  6/2015
Familial Cancer  6/2015
FEBS Letters  6/2015
Free Radical Research  6/2015
Frontiers in Bioscience  6/2015
Gene  6/2015
Genes and Development  10/2015
Genes, Chromosomes & Cancer  10/2015
Genesis  10/2015
Genetic Testing and Molecular Biomarkers  10/2015
Genetics  10/2015
Genetics in Medicine  10/2015
Genome Biology  10/2015
Genome Research  10/2015
Genomics  10/2015
Glycobiology  10/2015
Human Genetics  10/2015
Human Genome Variation  10/2015
Human Genomics  10/2015
Human Heredity  10/2015
Human Molecular Genetics  10/2015
Human Mutation  10/2015
Immunity  10/2015
Immunogenetics  10/2015
In Silico Biology  10/2015
Journal of Andrology  10/2015
Journal of Biological Chemistry (JBC)  10/2015
Journal of Cell Biology (JCB)  10/2015
Journal of Clinical Investigation  10/2015
Journal of Experimental Medicine  10/2015
Journal of Hematology & Oncology  10/2015
Journal of Heredity  10/2015
Journal of Human Genetics  10/2015
Journal of Immunology  10/2015
Journal of Inherited Metabolic Disease  10/2015
Journal of Medical Genetics (JMG)  10/2015
Journal of Neuromuscular Diseases  10/2015
Journal of Neuroscience  10/2015
Journal of Orthopaedic Research  10/2015
Journal of the American Medical Association (JAMA)  10/2015
Mammalian Genome  10/2015
Mitochondrial DNA  10/2015
Molecular and Cellular Biology  10/2015
Molecular Biology and Evolution  10/2015
Molecular Biology of the Cell  10/2015
Molecular Cell  10/2015
Molecular Diagnosis and Therapy  10/2015
Molecular Genetics and Genomic Medicine  10/2015
Molecular Genetics and Metabolism  10/2015
Molecular Phylogenetics and Evolution  10/2015
Molecular Syndomology  10/2015
Molecular Therapy  10/2015
Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis  10/2015
Mutation Research - Genetic Toxicology and Environmental Mutagenesis  10/2015
Mutation Research - Reviews  10/2015
Nature  10/2015
Nature Biotechnology  10/2015
Nature Cell Biology  10/2015
Nature Genetics  10/2015
Nature Immunology  10/2015
Nature Medicine  10/2015
Nature Reviews Cancer  10/2015
Nature Reviews Drug Discovery  10/2015
Nature Reviews Genetics  10/2015
Nature Reviews Immunology  10/2015
Nature Reviews Microbiology  10/2015
Nature Reviews Molecular Cell Biology  10/2015
Nature Reviews Neuroscience  10/2015
Nature Structural & Molecular Biology  10/2015
Neurogenetics  10/2015
Neuromuscular Disorders  10/2015
Neuron  10/2015
New England Journal of Medicine  10/2015
Nucleic Acids Research (NAR)  10/2015
Oncogene  10/2015
Open Longevity Science  10/2015
Orphanet Journal of Rare Diseases  10/2015
Parasite Immunology  10/2015
Pharmacogenetics and Genomics  10/2015
Physiological Genomics  10/2015
PLoS Biology  10/2015
PLoS Computational Biology  10/2015
PLoS Genetics  10/2015
PLoS Medicine  10/2015
PLoS Neglected Tropical Diseases  10/2015
PLoS One  10/2015
PLoS Pathogens  10/2015
Proceedings of the National Academy of Sciences USA (PNAS)  10/2015
Psychiatric Genetics  10/2015
Public Health Genomics  10/2015
Radiation Research  10/2015
Scandinavian Journal of Immunology  10/2015
Science  10/2015
The Anatomical Record  10/2015
The EMBO Journal  10/2015
The FEBS Journal  10/2015
The Lancet  12/2014
The Open Bioinformatics Journal  12/2014
The Open Biomaterials Journal  12/2014
The Open Bone Journal  12/2014
The Open Enzyme Inhibition Journal  12/2014
Trends in Biochemical Sciences (TIBS)  12/2014
Trends in Biotechnology  12/2014
Trends in Cell Biology  12/2014
Trends in Genetics (TIG)  10/2015
Trends in Immunology  10/2015
Trends in Molecular Medicine  10/2015
Trends in Neurosciences  10/2015

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 (http://www.genenames.org/) and OMIM database reference numbers (http://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 (http://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; http://www.ebi.ac.uk/dgva/) or the Database of Genomic Structural Variation (dbVar) (http://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 (http://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 ( http://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 (http://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 (http://www.humanvariomeproject.org/resources/resources.html) or using the URL "GeneSymbol".lovd.nl (e.g. http://TP53.lovd.nl).