HUGO Gene Nomenclature Committee: Difference between revisions
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Revision as of 15:10, 28 May 2014
 | |
| Content | |
|---|---|
| Description | HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, RNA genes and pseudogenes, to allow unambiguous scientific communication. |
| Data types captured | Gene nomenclature |
| Organisms | Human |
| Contact | |
| Research center | EMBL-EBI, UK; |
| Primary citation | Gray & al. (2013)[1] |
| Access | |
| Website | www |
| Download URL | Statistics & Downloads Custom Downloads HGNC Biomart |
| Web service URL | rest |
| Tools | |
| Web | HGNC Comparison of Orthology Predictions, Symbol report search[2] |
| Miscellaneous | |
| Curation policy | Yes |
The HUGO Gene Nomenclature Committee (HGNC) approves a unique and meaningful name for every known human gene[3] based on a query of experts. In addition to a long name, the HGNC also assigns an abbreviation (referred to as symbol) to every gene. The HGNC is part of the Human Genome Organisation (HUGO).
Purpose
Especially gene abbreviations/symbols but also full gene names are often not specific for a single gene. A marked example is CAP which can refer to any of 6 different genes (BRD4, CAP1, LNPEP, PTPLA, SERPINB6, and SORBS1).
The HGNC short gene names, or gene symbols, unlike previously used or published symbols, are specifically assigned to one gene only. This can result in less common abbreviations being selected but reduces confusion as to which gene is referred to.
Naming guidelines
The HGNC summarises its approach to naming genes and assigning symbols (gene name abbreviations) as follows:
- gene symbols must be unique
- symbols should only contain Latin letters and Arabic numerals
- symbols should not contain punctuation or "G" for gene
- symbols do not contain any reference to the species they are encoded in, i.e. "H/h" for human
The full description of HGNC's nomenclature guidelines can be found on their web site [1]. HGNC advocates the appendices _v1, _v2,.. to distinguish between different splice variants and _pr1, _pr2,.. for promoter variants of a single gene.
HGNC also states that "gene nomenclature should evolve with new technology rather than be restrictive as sometimes occurs when historical and single gene nomenclature systems are applied."[4]
Comprehensive human gene naming guidelines were last published in 2002,[5] but the HGNC have subsequently issued guides to specific locus types such as endogenous retroviral loci,[6] structural variants [7] and non-coding RNAs.[8][9]
Naming procedure
When assigning new gene nomenclature the HGNC make efforts to contact authors who have published on the human gene in question by email, and their responses to the proposed nomenclature are requested. In order to work in a timely manner, there is typically a two week time limit to respond but the deadline can be extended. HGNC also coordinates with the related Mouse and Rat Genomic Nomenclature Committees, other database curators, and experts for given specific gene families or sets of genes.
Revision
The gene name revision procedure is similar to the naming procedure, but changing a standardised gene name after establishment of a consensus can create confusion and the merit of this is therefore controversial. For this reason the HGNC aims to change a gene name only if agreement for that change can be reached among a majority of researchers working on that gene.
See also
References
- ^ Gray, KA (2013 Jan). "Genenames.org: the HGNC resources in 2013". Nucleic acids research. 41 (Database issue): D545-52. PMID 23161694.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Wright, MW (2005 Nov). "HCOP: the HGNC comparison of orthology predictions search tool". Mammalian genome : official journal of the International Mammalian Genome Society. 16 (11): 827–8. PMID 16284797.
{{cite journal}}: Check date values in:|date=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ http://www.genenames.org/about/overview
- ^ Shows, TB; McAlpine, PJ; Boucheix, C; Collins, FS; Conneally, PM; Frézal, J; Gershowitz, H; Goodfellow, PN; et al. (1987). "Guidelines for human gene nomenclature. An international system for human gene nomenclature (ISGN, 1987)" (PDF). Cytogenetics and cell genetics. 46 (1–4): 11–28. PMID 3507270.
- ^ Wain, HM (Apr 2002). "Guidelines for human gene nomenclature". Genomics. 79 (4): 464–70. PMID 11944974.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Mayer, J (May 4, 2011). "A revised nomenclature for transcribed human endogenous retroviral loci". Mobile DNA. 2 (1): 7. PMID 21542922.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Seal, RL (May 1, 2013). "Vive la différence: naming structural variants in the human reference genome". Human genomics. 7: 12. PMID 23634723.
{{cite journal}}: Unknown parameter|coauthors=ignored (|author=suggested) (help) - ^ Wright, MW; Bruford, EA (Jan 2011). "Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature". Human genomics. 5 (2): 90–8. PMID 21296742.
- ^ Wright, MW (Apr 9, 2014). "A short guide to long non-coding RNA gene nomenclature". Human genomics. 8 (1): 7. PMID 24716852.