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. 2015 Jan;43(Database issue):D423-31.
doi: 10.1093/nar/gku1161. Epub 2014 Nov 20.

The IPD and IMGT/HLA database: allele variant databases

James Robinson  1 , Jason A Halliwell  2 , James D Hayhurst  2 , Paul Flicek  3 , Peter Parham  4 , Steven G E Marsh  5
Affiliations

The IPD and IMGT/HLA database: allele variant databases

James Robinson et al. Nucleic Acids Res. 2015 Jan.

Abstract

The Immuno Polymorphism Database (IPD) was developed to provide a centralized system for the study of polymorphism in genes of the immune system. Through the IPD project we have established a central platform for the curation and publication of locus-specific databases involved either directly or related to the function of the Major Histocompatibility Complex in a number of different species. We have collaborated with specialist groups or nomenclature committees that curate the individual sections before they are submitted to IPD for online publication. IPD consists of five core databases, with the IMGT/HLA Database as the primary database. Through the work of the various nomenclature committees, the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. The IPD project continues to develop with new tools being added to address scientific developments, such as Next Generation Sequencing, and to address user feedback and requests. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.

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Figures

Figure 1.
Figure 1.
Growth of the IMGT/HLA Database. The number of allele sequences deposited annually in the IMGT/HLA Database is shown for class I (green), class II (black). The slope of the line reflects the rate of acquisition, which has accelerated in recent years.
Figure 2.
Figure 2.
Sequence Coverage of HLA-B in the IMGT/HLA Database. Panel (A) represent the HLA-B CDS sequences in the database, Panel (B) represents the HLA-B gDNA sequences. The white areas represent the unsequenced regions. The black areas represent the sequenced regions. The sequences are ordered by the length of sequence covered, the plots clearly show the exon 2 and 3 regions which are mandatory requirements for submission to the IMGT/HLA Database.
Figure 3.
Figure 3.
IMGT/HLA HGVS Variant Report. The figure shows an example of an allele report, which utilizes the HGVS variant reporting format to describe the allele rather than display the entire sequence. The variations are described in relation to the WHO HLA Reference Sequence and a GRC reference sequence.
See this image and copyright information in PMC

References

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