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The IPD and IMGT/HLA database: allele variant databases.

Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG - Nucleic Acids Res. (2014)

Bottom Line: 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.Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.

View Article: PubMed Central - PubMed

Affiliation: Anthony Nolan Research Institute, Hampstead, London, NW3 2QG, UK UCL Cancer Institute, University College London, Hampstead, London, NW3 2QG, UK.

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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.
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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.

Mentions: The IMGT/HLA Database was established to provide a locus-specific database (LSDB) for the allelic sequences of the genes in the HLA system, also known as the human MHC. The IMGT/HLA Database was first released in 1998 and subsequently incorporated as a module of IPD in 2012. The MHC is one of the most complex and polymorphic regions of the human genome, with in excess of 220 genes (2). The core genes of interest in the HLA system are 21 polymorphic HLA genes, found within the 6p21.3 region of the short arm of human chromosome 6, whose protein products mediate human responses to infectious disease and influence the outcome of cell and organ transplants. The level of polymorphism seen in some of the genes is very high, with over 3000 variants seen in HLA-B; this level of variation can be considered hyper-polymorphic when compared to other gene systems. Three distinct regions have been identified within the MHC. The class I region is located at the telomeric end of the MHC and encodes the genes for the HLA class I molecules, HLA-A, -B and -C. These are co-dominantly expressed on the cell surface, and are responsible for presenting intracellularly derived peptides to CD8 positive T cells. The class II region lies at the centromeric end of the MHC and encodes HLA class II genes HLA-DRA, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1 and -DPB1. HLA class II expression is limited to professional antigen presenting cells, where these molecules present extracellularly derived peptides to CD4 positive T cells. Located between the class I and class II regions lies the class III region where a number of non-HLA genes with immune function are located. With a nomenclature covering more than 50 genes and 12 000 alleles, there is an obvious need for a curated LSDB to manage these highly polymorphic variants. The first public release of the IMGT/HLA Database was made on the 16 December 1998 (3). Since then the database has been updated every three months, in a total of 64 releases, (Figure 1), to include all the publicly available sequences officially named by the WHO Nomenclature Committee at the time of release.


The IPD and IMGT/HLA database: allele variant databases.

Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG - Nucleic Acids Res. (2014)

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.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383959&req=5

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.
Mentions: The IMGT/HLA Database was established to provide a locus-specific database (LSDB) for the allelic sequences of the genes in the HLA system, also known as the human MHC. The IMGT/HLA Database was first released in 1998 and subsequently incorporated as a module of IPD in 2012. The MHC is one of the most complex and polymorphic regions of the human genome, with in excess of 220 genes (2). The core genes of interest in the HLA system are 21 polymorphic HLA genes, found within the 6p21.3 region of the short arm of human chromosome 6, whose protein products mediate human responses to infectious disease and influence the outcome of cell and organ transplants. The level of polymorphism seen in some of the genes is very high, with over 3000 variants seen in HLA-B; this level of variation can be considered hyper-polymorphic when compared to other gene systems. Three distinct regions have been identified within the MHC. The class I region is located at the telomeric end of the MHC and encodes the genes for the HLA class I molecules, HLA-A, -B and -C. These are co-dominantly expressed on the cell surface, and are responsible for presenting intracellularly derived peptides to CD8 positive T cells. The class II region lies at the centromeric end of the MHC and encodes HLA class II genes HLA-DRA, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1 and -DPB1. HLA class II expression is limited to professional antigen presenting cells, where these molecules present extracellularly derived peptides to CD4 positive T cells. Located between the class I and class II regions lies the class III region where a number of non-HLA genes with immune function are located. With a nomenclature covering more than 50 genes and 12 000 alleles, there is an obvious need for a curated LSDB to manage these highly polymorphic variants. The first public release of the IMGT/HLA Database was made on the 16 December 1998 (3). Since then the database has been updated every three months, in a total of 64 releases, (Figure 1), to include all the publicly available sequences officially named by the WHO Nomenclature Committee at the time of release.

Bottom Line: 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.Regular updates to the website ensure that new and confirmatory sequences are dispersed to the immunogenetics community, and the wider research and clinical communities.

View Article: PubMed Central - PubMed

Affiliation: Anthony Nolan Research Institute, Hampstead, London, NW3 2QG, UK UCL Cancer Institute, University College London, Hampstead, London, NW3 2QG, UK.

Show MeSH