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HLA Typing pp 31-48 | Cite as

The IPD Databases: Cataloguing and Understanding Allele Variants

  • Jashan P. Abraham
  • Dominic J. Barker
  • James Robinson
  • Giuseppe Maccari
  • Steven G. E. MarshEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

The IMGT/HLA Database has provided a repository for information regarding polymorphism in the genes of the immune system since 1998. In 2003, it was absorbed into the Immuno Polymorphism Database (IPD). The IPD project has enabled us to create and maintain a platform for curating and publishing locus-specific databases which are either involved directly with, or relate to, the function of the Major Histocompatibility Complex across a number of species. In collaboration with specialist groups and nomenclature committees individual sections have been curated prior to their submission to the IPD for online publication. The IPD consists of five core databases, with the primary database being the IMGT/HLA Database. With the work of various nomenclature committees, the HLA Informatics Group, and alongside the European Bioinformatics Institute, we provide access to this data through the website (http://www.ebi.ac.uk/ipd/) to the public domain. The IPD project continually develops new tools in conjunction with on-going scientific developments—such as Next-Generation Sequencing—to maintain efficiency and usability in response to user feedback and requests. The website is updated on a regular basis to ensure that new and confirmatory sequences are distributed to the immunogenetics community, as well as the wider research and clinical communities.

Keywords

HLA KIR MHC Alleles Variants Transplantation Database 

Notes

Acknowledgments

We would like to acknowledge the work of all the individual nomenclature committees. We would also like to acknowledge the support provided by the European Molecular Biology Laboratory’s European Bioinformatics Institute—in particular, Paul Fliceck—which allows the IPD project to be hosted within the EBI infrastructure.

We also recognize the work of Libby Guethlein and Peter Parham at Stanford University Medical School on IPD-KIR, IPD-MHC and IPD-KIR, IPD-HLA respectively and Jeff Miller and Sarah Cooley at the University of Minnesota on IPD-KIR, as well as the individual IPD-MHC Nomenclature committees and curators for their work in collaboration with the IPD-MHC Database.

The authors would like to thank Todd Peterson of the Be The Match Foundation, for his work in securing on going funding for the database. We would like to thank all of the individuals and organizations that support our work financially.

Funding

European Commission within the Fifth Framework Infrastructures program [QLRI-CT-2001-01325 to IPD projects for IPD-ESTDAB]; National Institutes of Health [NIH/NCI P01 111412 to IPD projects for IPD-ESTDAB]. International Union of Immunological Societies (IUIS) for KIR nomenclature through the IUIS KIR Nomenclature Committee and MHC Nomenclature by the International Society for Animal Genetics (ISAG) and the Veterinary Immunology Committee (VIC) [to IPD databases]. One Lamda Inc.; Histogenetics; DKMS; American Society for Histocompatibility and Immunogenetics; FujireBio; European Federation for Immunogenetics; Olerup SSP; LabCorp; Zentrales Knochenmarkspender-Register Deutschland; Lifecodes + ImmucorGamma; Illumina; Omixon Biocomputing; Roche; Anthony Nolan; Asia-Pacific Histocompatibility and Immunogenetics Association; BAG Healthcare; Be the Match Foundation; Linkage Biosciences; National Marrow Donor Program; GenDx; Imperial Cancer Research Fund (now Cancer Research UK); EU Biotech [BIO4CT960037; all to the IPD-IMGT/HLA Database project].

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Jashan P. Abraham
    • 1
  • Dominic J. Barker
    • 1
  • James Robinson
    • 1
    • 2
  • Giuseppe Maccari
    • 1
    • 3
  • Steven G. E. Marsh
    • 1
    • 2
    Email author
  1. 1.Anthony Nolan Research InstituteLondonUK
  2. 2.UCL Cancer InstituteUniversity College LondonLondonUK
  3. 3.The Pirbright InstituteSurreyUK

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