The IMGT/HLA database - PubMed (original) (raw)
. 2009 Jan;37(Database issue):D1013-7.
doi: 10.1093/nar/gkn662. Epub 2008 Oct 5.
Affiliations
- PMID: 18838392
- PMCID: PMC2686596
- DOI: 10.1093/nar/gkn662
The IMGT/HLA database
James Robinson et al. Nucleic Acids Res. 2009 Jan.
Abstract
It is 10 years since the IMGT/HLA database was released, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic. The naming of these HLA genes and alleles, and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of 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/imgt/hla/. The first release contained 964 sequences, the most recent release 3300 sequences, with around 450 new sequences been added each year. The tools provided on the website have been updated to allow more complex alignments, which include genomic sequence data, as well as the development of tools for probe and primer design and the inclusion of data from the HLA Dictionary. Regular updates to the website ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.
Figures
Figure 1.
Section of an HLA allele report. The report provides cross-references to a text flat-file in SRS (HLA0001), the OMIM entry for HLA-A, the source entries in EMBL-Bank (AJ278305-Z93949) and to the seminal citations in PubMed. Other information provided includes links to the source material the sequence was derived from. The full entry also contains the nucleotide sequence at both the CDS and genomic level.
Figure 2.
CDS HLA Allele alignment indicating the alternatively spliced allele, A*0111N. The alternatively spliced A*0111N allele is shown aligned to the reference allele A*01010101. Identity to the A*01010101 allele is shown by hyphens (-) and the exon borders are indicated by a pipe (|). The single nucleotide mutation in the third base of codon 175, introduces a new splice site and as a result the region shaded in green is spliced out and is not part of the CDS. It is helpful to include the otherwise missing sequence and highlight it to emphasize the region of interest, rather than omit it, this feature is important for the design of reagents to allow for typing of this allele.
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References
- Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot C.C., Jr, Wright MW, et al. Gene map of the extended human MHC. Nat. Rev. Genet. 2004;5:889–899. - PubMed
- Orr HT, Lopez de Castro JA, Lancet D, Strominger JL. Complete amino acid sequence of a papain-solubilized human histocompatibility antigen, HLA-B7. 2. Sequence determination and search for homologies. Biochemistry. 1979;18:5711–5720. - PubMed
- Lee JS, Trowsdale J, Travers PJ, Carey J, Grosveld F, Jenkins J, Bodmer WF. Sequence of an HLA-DR alpha-chain cDNA clone and intron-exon organization of the corresponding gene. Nature. 1982;299:750–752. - PubMed
- Payne R, Bodmer WF, Troup GM, Walford RL. Serologic activities and specificities of eleven human leukocyte antisera produced by planned immunization. Transplantation. 1967;5:597–605. - PubMed
- Bodmer WF, Albert E, Bodmer JG, Dupont B, Mach B, Mayr WR, Sasazuki T, Schreuder GMT, Svejgaard A, Terasaki PI. In: Immunobiology of HLA. Dupont B, editor. Vol. 1. New York: Springer; 1989. pp. 72–79.
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