IPD-MHC Database

IUIS Veterinary Immunology Committee (VIC) is committed to promoting open access to databases and analysis tools. Recently we supported the IPD-MHC database which continues to provide an open, community-oriented and manually curated resource for the study of MHC.

The major histocompatibility complex (MHC) is a highly variable region of all vertebrate genomes encoding genes that dictate how an individual’s immune system responds to challenge. Therefore, a greater understanding of this diversity to enable us to improve disease outcome requires bespoke databases and tools.

The IPD-MHC database is the reference repository of non-human MHC genes and includes the major farmed animal species (cattle, sheep, goat, chicken, pigs, trout and salmon), as well as companion (dog, horse) and medical (rat, non-human primates). Together with the collection and analysis of the MHC genes, the IPD-MHC Database acts as the official repository of non-human MHC nomenclature, manually curated by experts in the field and overseen by the MHC Nomenclature Committee.

In 2015, the IPD-MHC Database was awarded a UK’s Biotechnology and Biological Sciences Research Council (BBSRC) grant to support its upgrade and future development to help adapt to the advances in sequencing technology and the growth in comparative immunology. As a result, the database was redesigned to allow the collection and comparison of genomic and non-genomic sequences and provide tools for the inter- and intraspecies comparison of allele variation. This enhanced functionality has required a new level of standardisation in the MHC nomenclature between species and taxonomic groups to allow an unambiguous inter- and intra- species comparison of alleles. Following some support from the IUIS-VIC, a centralised set of tools was introduced to help curators from all over the world to annotate and name MHC sequences from a variety set of organisms, at the same time providing a framework for the futureproofing and expansion of the project.

The IPD-MHC Database is now generating a renewed interest, both in database traffic and in the increasing amount of submitted data. Since its update in 2016, the number of visits per year has doubled to more than 200,000. This is particularly true for livestock and farmed species, where the number of submitted sequences and curated alleles has also more than doubled.