The IMGT/HLA database

By James Robinson, M. Waller, Sylvie C. Fail, Hamish McWilliam, Rodrigo Lopez, Peter Parham, Steven G. E. Marsh. Nucleic Acids Res., 2008

1,040 citations recorded by the source corpus.

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.

Subfields: Immunology

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In Immunology

Citations in the corpus

Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis (2012, methodology): “To test this, we repeatedly reassigned amino acid sequences to each of the classical HLA-DRB1 alleles (as defined in the standard HLA dictionar”
pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens (2016, methodology): “…(1) We performed the alignment step, in which exome sequence data from the normal tissue sample are aligned against reference HLA allele sequences present in the IMGT/HLA database [27], using BWA with zero mismatches ( params : bwa aln -e 0 -o 0 -n 0 ) instead of NovoAlign [28] with one mismatch.”
Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens (2013, methodology): “Second, we extracted the unique DNA and amino acid sequences for all observed HLA alleles from the EMBL-EBI Immunogenetics HLA Database [39] (http://www.ebi.ac.uk/imgt/hla/), and encoded polymorphic nucleotide and amino acid positions as binary markers in the reference panel.”
Nomenclature for factors of the HLA system, 2010 (2010, methodology): “The database contains sequences for all HLA alleles officially recognised by the WHO Nomenclature Committee for Factors of the HLA System and provides users with online tools and facilities for their retrieval and analysis.”
OptiType: precision HLA typing from next-generation sequencing data (2014, background): “Both HLA classes comprise three major loci (HLA-I: A, B, C; HLA-II: DP, DQ, DR), which are co-dominantly expressed.”
Major Histocompatibility Complex Genomics and Human Disease (2013, neutral): “It is regularly updated, and an international committee meets periodically to standardize the nomenclature (102).”
RefSeq: an update on mammalian reference sequences (2013, background): “Information System (IMGT) (3), miRBase (4) and pseudogene.”
Peptide Vaccine: Progress and Challenges (2014, background): “database, which gives information of MHC alleles and its polymorphism and distribution in the community, is useful for this purpose [36].”
IPD—the Immuno Polymorphism Database (2012, methodology): “The nomenclature for MHC genes and alleles in species other than humans (20,21) and mice (22,23) has historically been overseen either informally by groups generating sequences, or by formal nomenclature committees set up by the International Society for Animal Genetics (ISAG) (24).”
HIBAG – HLA Genotype Imputation with Attribute Bagging (2013, neutral): “The numbers of HLA alleles documented in the IMGT-HLA database 2 are much larger than the numbers investigated in our study.”
The IPD and IMGT/HLA database: allele variant databases (2014, background): “This means that users are free to copy, distribute, display and make commercial use of the databases in all jurisdictions provided they give the appropriate credit (52,53).”