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. 2023 Jan 6;51(D1):D1053-D1060.
doi: 10.1093/nar/gkac1011.

The IPD-IMGT/HLA Database

Dominic J Barker  1   2 , Giuseppe Maccari  3 , Xenia Georgiou  1 , Michael A Cooper  1 , Paul Flicek  4 , James Robinson  1   2 , Steven G E Marsh  1   2
Affiliations

The IPD-IMGT/HLA Database

Dominic J Barker et al. Nucleic Acids Res. .

Abstract

It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.

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Figures

Figure 1.
Figure 1.
Growth of the database in the number of alleles per year. Growth split into HLA class I (green) and HLA class II (black). The latest year (2022) is extrapolated for the end of the year in lighter shades.
Figure 2.
Figure 2.
Increasing use of NGS technologies in submissions to the IPD-IMGT/HLA Database. From 2000–2016 Sanger sequencing (green) was the dominant method in determining HLA sequences. Since 2016 there has been a sharp increase in NGS technologies starting with Illumina (light blue) and then PacBio (yellow). The increasing use of NGS technologies has resulted in an increased rate of nucleotide growth (dark blue line) in the database. Numbers of nucleotides in the database are given per year from 2010.
Figure 3.
Figure 3.
The IPD API provides information both for allele and cell data. (A) Data is stored in a MongoDB database and is served through an API that can be accessed either programmatically or through a series of tools available on the official website. The Matching API functions in tandem with the IPD API providing a secondary entry point which includes specific logic to determine the matching criteria of patients and donors. (B) The API provides a powerful query schema that allows to virtually filter for any bit of information available on the database, providing a powerful tool for the study of genetic polymorphism in the immune system.
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References

    1. Robinson J., Bodmer J.G., Malik K., Marsh S.G.E.. Development of the international immunogenetics HLA database. Hum. Immunol. 1998; 59:17.
    1. Robinson J., Malik A., Parham P., Bodmer J.G., Marsh S.G.E.. IMGT/HLA - a sequence database for the human major histocompatibility complex. Tissue Antigens. 2000; 55:280–287. - PubMed
    1. Ruiz M., Giudecelli V., Ginestoux C., Stoehr P., Robinson J., Bodmer J., Marsh S.G.E., Bontrop R., Lemaitre M., Lefranc G.et al. .. IMGT, the international immunogenetics database. Nucleic Acids Res. 2000; 28:219–221. - PMC - PubMed
    1. Marsh S.G.E., Robinson J.. The IMGT/HLA sequence database. Rev. Immunogenet. 2000; 2:518–531. - PubMed
    1. Robinson J., Waller M.J., Parham P., Bodmer J.G., Marsh S.G.E.. IMGT/HLA - a sequence database for the human major histocompatibility complex. Nucleic Acids Res. 2001; 29:210–213. - PMC - PubMed

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