The imgt/HLA database

Anthony Nolan Research Institute, Royal Free Hospital, Pond Street, Hampstead, London NW3 2QG, UK.
Nucleic Acids Research (Impact Factor: 9.11). 11/2010; 39(Database issue):D1171-6. DOI: 10.1093/nar/gkq998
Source: PubMed


It is 12 years since the IMGT/HLA database was first 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 web site Regular updates to the web site ensure that new and confirmatory sequences are dispersed to the HLA community, and the wider research and clinical communities.

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    • "http://www. (Robinson et al. 2011). In comparison, the overall structure of the MHC class I regions in the rhesus macaques (Daza-Vamenta et al. 2004) is more complex than the HLA (Shiina et al. 1999) and the common chimpanzee MHC (Patr) (Anzai et al. 2003) because the macaques carry many more duplicated MHC class I genes than humans and chimpanzees. "
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    ABSTRACT: Although the low polymorphism of the major histocompatibility complex (MHC) transplantation genes in the Filipino cynomolgus macaque (Macaca fascicularis) is expected to have important implications in the selection and breeding of animals for medical research, detailed polymorphism information is still lacking for many of the duplicated class I genes. To better elucidate the degree and types of MHC polymorphisms and haplotypes in the Filipino macaque population, we genotyped 127 unrelated animals by the Sanger sequencing method and high-resolution pyrosequencing and identified 112 different alleles, 28 at cynomolgus macaque MHC (Mafa)-A, 54 at Mafa-B, 12 at Mafa-I, 11 at Mafa-E, and seven at Mafa-F alleles, of which 56 were newly described. Of them, the newly discovered Mafa-A8*01:01 lineage allele had low nucleotide similarities (<86 %) with primate MHC class I genes, and it was also conserved in the Vietnamese and Indonesian populations. In addition, haplotype estimations revealed 17 Mafa-A, 23 Mafa-B, and 12 Mafa-E haplotypes integrated with 84 Mafa-class I haplotypes and Mafa-F alleles. Of these, the two Mafa-class I haplotypes, F/A/E/B-Hp1 and F/A/E/B-Hp2, had the highest haplotype frequencies at 10.6 and 10.2 %, respectively. This suggests that large scale genetic screening of the Filipino macaque population would identify these and other high-frequency Mafa-class I haplotypes that could be used as MHC control animals for the benefit of biomedical research.
    Immunogenetics 09/2015; 67(10). DOI:10.1007/s00251-015-0867-9 · 2.23 Impact Factor
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    • "HLA-A ⁄ 23:19Q was first assigned in 2007 as a questionable allele due to its unknown surface expression. The allele has been found in 7 different individuals and was confirmed in 4 laboratories by sequence analysis, although only partial allele sequences have been submitted (exons 2, 3 and 4) [1]. We encountered this allele, GD23Q: HLA-A ⁄ 23:19Q, 29:02:01, in a sample of the Guadeloupe population [11] [12]. "
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    ABSTRACT: The assignment of null alleles is clinically relevant in stem cell transplantation, in particular for donor selection. It is unclear how questionable (Q) alleles, having an unknown expression profile, should be considered in matching criteria. In this study we analyzed the RNA and protein expression profile of a questionable allele encountered in a sample of the Guadeloupe population: GD23Q, HLA-A∗23:19Q, 29:02:01. Full-length DNA sequencing of HLA-A∗23:19Q revealed a single polymorphism at position 619 (G > A) compared to HLA-A∗23:01:01. Serological typing showed only the presence of HLA-A29; HLA-A∗23:19Q was not detected on the cell surface. The absence of HLA-A∗23:19Q surface expression was shown by flow cytometry using a directly labeled monoclonal antibody and a panel of five indirectly labeled polyclonal antibodies all directed against HLA-A23 (HLA-A9) molecules. Allele specific amplification revealed the absence of intact full-length mRNA, but the presence of two major alternatively spliced mRNAs: sequencing identified that in one variant exon 3 is missing and in the other variant introns 2 and 3 are retained. Based upon the lack of HLA-A∗23:19Q surface expression and the presence of aberrant mRNA transcripts only, this study shows that HLA-A∗23:19Q is non-expressed.
    Human Immunology 02/2015; 76(4). DOI:10.1016/j.humimm.2015.02.001 · 2.14 Impact Factor
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    • "The assorted affinities within the binding grooves of HLA molecules control the repertoire of bound epitopes and shape immune response profiles. HLA genes located in the human major histocompatibility complex (MHC; 6p21.3) are highly polymorphic , with more than 5000 alleles identified for the class I HLA alleles alone [9]. Given the HLA alleles frequencies from any one population, random mating can result in billions of possible genotype combinations. "
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    ABSTRACT: We have estimated human leukocyte antigen (HLA) haplotype frequencies using the maximum likelihood mode, which accommodates typing ambiguities. The results of the frequency distribution of the 7,015 haplotypes obtained are presented here. These include a total of 114 HLA-A, 185 HLA-B, and 76 HLA-DRB1 unique alleles at each locus. Across all populations, although the most common individual HLA alleles were HLA-A∗02:01 (29.0%), HLA-B∗07:02 (11.4%), and HLA-DRB1∗07:01 (15.9%), the most frequent haplotype was found to be HLA-A∗01:01-B∗08:01-DRB1∗03:01. Copyright © 2015. Published by Elsevier Inc.
    Human Immunology 01/2015; 76(5). DOI:10.1016/j.humimm.2015.01.028 · 2.14 Impact Factor
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