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dc.contributor.authorAfrache, Hassnaeen
dc.contributor.authorTregaskes, Cliveen
dc.contributor.authorKaufman, Jimen
dc.date.accessioned2019-10-29T00:31:26Z
dc.date.available2019-10-29T00:31:26Z
dc.date.issued2020-02en
dc.identifier.issn0093-7711
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/298146
dc.description.abstractAmong the genes with the highest allelic polymorphism and sequence diversity are those encoding the classical class I and class II molecules of the major histocompatibility complex (MHC). Although many thousands of MHC sequences have been deposited in general sequence databases like GenBank, the availability of curated MHC sequences with agreed nomenclature has been enormously beneficial. Along with the immunogenetics-human leukocyte antigen (IMGT-HLA) database, a collection of databases for curated sequences of immune importance is available as the immunopolymorphism database (IPD). A recent addition is an IPD-MHC database for chickens. For many years, the nomenclature system for chicken MHC genes has been based on a list of standard, presumed to be stable, haplotypes. However, these standard haplotypes give different names to identical sequences. Moreover, the discovery of new recombinants between haplotypes and a rapid increase in newly-discovered alleles leaves the old system untenable. In this review, a new nomenclature is considered, for which alleles of different loci are given names based on the system used for other MHCs, and then haplotypes are named according to the alleles present. The new nomenclature system is trialed, first with standard haplotypes and then with validated sequences from the scientific literature. In the trial, some class II B sequences were found in both class II loci, presumably by gene conversion or inversion, so that identical sequences would receive different names. This situation prompts further suggestions to the new nomenclature system. In summary, there has been progress but also problems with the new IPD-MHC system for chickens.
dc.description.sponsorshipWellcome Trust Investigator Award (110106/Z/15/Z)
dc.format.mediumPrint-Electronicen
dc.languageengen
dc.publisherSpringer Nature
dc.rightsAll rights reserved
dc.rights.uri
dc.subjectAnimalsen
dc.subjectChickensen
dc.subjectImmunogeneticsen
dc.subjectMajor Histocompatibility Complexen
dc.subjectPolymorphism, Geneticen
dc.subjectDatabases, Factualen
dc.subjectTerminology as Topicen
dc.titleA potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems.en
dc.typeArticle
prism.endingPage24
prism.issueIdentifier1-2en
prism.publicationDate2020en
prism.publicationNameImmunogeneticsen
prism.startingPage9
prism.volume72en
dc.identifier.doi10.17863/CAM.45203
dcterms.dateAccepted2019-10-20en
rioxxterms.versionofrecord10.1007/s00251-019-01145-6en
rioxxterms.versionAM
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserveden
rioxxterms.licenseref.startdate2020-02en
dc.contributor.orcidTregaskes, Clive [0000-0002-5750-0853]
dc.contributor.orcidKaufman, James [0000-0002-7216-8422]
dc.identifier.eissn1432-1211
rioxxterms.typeJournal Article/Reviewen
pubs.funder-project-idWELLCOME TRUST (110106/Z/15/Z)
cam.orpheus.successThu Jan 30 10:36:31 GMT 2020 - Embargo updated*
rioxxterms.freetoread.startdate2020-11-18


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