The Genenames Blog
The Genenames blog was established in April 2019 and has been set up to engage with researchers, promoting the use of standardized gene nomenclature for human and across [VGNC] (https://vertebrate.genenames.org/) vertebrate species.
It is now the new home for our newsletters and will also be used to publish “how-to” guides for our website, alert a wider audience to recent gene nomenclature changes, host guest posts from our collaborators and highlight contents of talks and posters from conferences that we attend.
We have incorporated the Disqus comment plug-in, so that users can comment on our blog posts (which will be pre-moderated before appearing on the site).
Our newsletter archive is still available, if you wish to re-read previous pre-blog editions of our news reports.
We will tweet about every new blog post that we create, so please make sure that you are following our @genenames Twitter account!
The HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.
For each known human gene we approve a gene name and symbol (short-form abbreviation). All approved symbols are stored in the HGNC database, https://www.genenames.org, a curated online repository of HGNC-approved gene nomenclature, gene groups and associated resources including links to genomic, proteomic and phenotypic information. Each symbol is unique and we ensure that each gene is only given one approved gene symbol. It is necessary to provide a unique symbol for each gene so that we and others can talk about them, and this also facilitates electronic data retrieval from publications and databases. In preference each symbol maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse.
We have already approved almost 33,000 symbols; the vast majority of these are for protein-coding genes, but also include symbols for pseudogenes, non-coding RNAs, phenotypes and genomic features (see HGNC Search). Individual new symbols are requested by scientists, journals (e.g. Genomics, Nature Genetics) and databases (e.g.Ensembl, Entrez Gene, MGI, RGD and OMIM), and groups of new symbols by those working on gene groups or specific regions of the genome. In all cases considerable efforts are made to use a symbol acceptable to workers in the field.
The Vertebrate Gene Nomenclature Committee (VGNC) is an extension of the established HGNC (HUGO Gene Nomenclature Committee) project that names human genes. VGNC is responsible for assigning standardized names to genes in vertebrate species that currently lack a nomenclature committee. The VGNC also coordinates with the 5 existing active vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs.
The VGNC uses a software pipeline based on the HGNC Consensus Orthology Predictions (HCOP) tool to transfer human nomenclature to other species automatically for genes where the same orthologs are predicted by four different resources (Ensembl, NCBI Gene, OMA and PANTHER). For genes where there is no such consensus ortholog prediction, naming is based on a combination of a semi-automated pipeline and manual curation, taking into account synteny, phylogeny and other data. We also rely on the expertise of specialist advisors for naming within complex families. Two key complex families are the olfactory receptors (ORs) - the largest family in mammalian genomes - and the cytochrome P450s (CYPs); we are collaborating with Drs David Nelson and Jed Goldstone for the CYPs and Drs Doron Lancet and Tsviya Olender for the ORs.
The current species for VGNC naming are chimpanzee, horse, cow and dog and this naming process will be extended to other species in due course. Our criteria for choosing further vertebrate species are the quality of the genome assembly and annotation, the perceived value as a research organism and the level of support from the scientific community. Please contact us at firstname.lastname@example.org with suggestions on which species should be our next choices for gene naming.