IPD-MHC: nomenclature requirements for the non-human major histocompatibility complex in the next-generation sequencing era

Immunogenetics
Giuseppe MaccariJohn A Hammond

Abstract

The IPD-MHC Database is the official repository for non-human MHC sequences, overseen and supported by the Comparative MHC Nomenclature Committee, providing access to curated MHC data and associated analysis tools. To address the increasing amount and complexity of data being submitted, an entirely upgraded version of the IPD-MHC Database was recently released to maintain IPD-MHC as the central platform for the comparison of curated MHC data. As a consequence, a new level of nomenclature standardisation is required between the different species to enable data submission and to allow the unambiguous inter- and intra-species comparison of alleles. However, any changes must retain the flexibility demanded by the unique biology of different taxonomic groups. Here, we describe the rationale for a standardised nomenclature system and summarise the changes that have been driven by the requirements of implementing the IPD-MHC database. This modified nomenclature system is essential to maintain the current functionality of IPD-MHC and provide a scalable future-proof database organisation to fully exploit the bioinformatic tools used for analysis.

References

Jan 10, 2003·Nucleic Acids Research·James RobinsonSteven G E Marsh
Dec 21, 2004·Nucleic Acids Research·James RobinsonSteven G E Marsh
Jan 4, 2006·Immunogenetics·Shirley A EllisUNKNOWN ISAG/IUIS-VIC Comparative MHC Nomenclature Committee
Apr 2, 2010·Tissue Antigens·S G E MarshJ Trowsdale
May 14, 2011·Genome Research·Bridgett M vonHoldtRobert K Wayne
Dec 3, 2016·Nucleic Acids Research·Giuseppe MaccariSteven G E Marsh
Jul 25, 2018·Immunogenetics·Keith T BallingallSteven G E Marsh

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Citations

Nov 13, 2019·Immunogenetics·Arvind Y M SundaramUnni Grimholt
Dec 18, 2019·Annual Review of Animal Biosciences·Sabine E HammerJoan K Lunney
Nov 12, 2018·Immunogenetics·Keith T BallingallLynne Herrmann-Hoesing
Apr 26, 2019·Frontiers in Immunology·André Luiz Alves de SáMaria Paula Cruz Schneider
Jul 25, 2018·Immunogenetics·Keith T BallingallSteven G E Marsh
Jan 31, 2021·BMC Ecology and Evolution·U Grimholt, M Lukacs
Jun 9, 2021·HLA : Immune Response Genetics·Deepali VasoyaTimothy Connelley
Jan 31, 2019·Journal of Proteome Research·Yanjuan LiQuan Zou
Nov 22, 2021·HLA : Immune Response Genetics·John C SchwartzJohn A Hammond

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Software Mentioned

MHC
Comparati
IPD

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