Go to the abstract in the NAR 2003 Database Issue.
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http://www.ebi.ac.uk/imgt/hla/
Robinson, J.1, Waller, MJ.1, Parham, P.2, Stoehr, P.3, Marsh, SGE.1
1Anthony Nolan Research Institute, Royal Free Hospital, London, United Kingdom
2Department of Structural Biology and Microbiology and Immunology, Stanford University, CA, USA
3European Bioinformatics Institute, Cambridge, UK
Contact jrobinso@ebi.ac.uk
The HLA complex is located within the 6p21.3 region on the short arm of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and include many highly polymorphic HLA genes. These genes influence the outcome of clinical transplantation and confer susceptibility to a wide range of non-infectious diseases. The responsibility for naming genes and alleles of the HLA system lies with the WHO Nomenclature Committee for Factors of the HLA System, who have for over thirty years undertaken this effort. There are currently over 1500 officially recognised HLA alleles and these sequences are made available to the scientific community through the IMGT/HLA database. In 1998 the IMGT/HLA database was publicly released. Since this time the database has grown and is the primary source of information for the study of sequences of the human major histocompatibilty complex. The initial release of the database contained a limited number of tools. These included allele reports, alignment tools, submission tools as well as detailed descriptions of the source cells. The latest releases of the database demonstrate how, as a result of feedback from our users, we have been able to provide new tools and facilities for the study of HLA sequences. The database still provides the basic tools needed to retrieve allele information and to perform sequence alignments, although these tools have been improved since the initial release. We also now provide more tools to support the identification and analysis of alleles. This includes online searches of the ambiguous typing combinations as found in sequencing based typing (SBT), as well as polymorphism identification tools, to aid in the analysis of new sequences. The HLA sequences themselves have also been extended to include intron sequences and the 3’ and 5’ untranslated regions into the alignments and also the inclusion of new genes such as MICA. The database is updated quarterly with all the new and confirmatory sequences submitted to the WHO Nomenclature Committee and on average an additional 75 new and confirmatory sequences are included in each quarterly release. Submission of HLA sequences to the committee is only possible through the tools provided by the IMGT/HLA database. The submission tool has also been updated to incorporate the submission of genomic sequences. The tool also now has predictive labelling of sequence features, to speed up the submission of genomic sequences. The IMGT/HLA database provides a centralised resource for everybody interested, either centrally or peripherally, in the HLA system. The database and accompanying tools allow the study of HLA alleles from a single site on the World Wide Web. It should aid in the management and continual expansion of the HLA nomenclature, providing an ongoing resource for the WHO Nomenclature Committee. The database will also act as a model system for the development of similar projects in other species.
The IMGT/HLA database has been expanded to include intronic sequences for some of the loci. The majority of tools have also been updated as a result of user feedback. New tools added include analysis of the ambiguous allele combinations, as found in sequencing based typing (SBT) and tools for the identification of polymorphic sites. The submission tool has also been updated to assist in the submission of genomic sequences.
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Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE. Tissue Antigens (2000), 55:280-287
Robinson J, Waller MJ, Parham P, Bodmer JG, Marsh SGE. Nucleic Acids Research (2001), 29:210-213
Marsh SGE, Robinson J. Reviews in Immunogenetics (2001) 2:518-531
Category Protein Databases
Go to the abstract in the NAR 2003 Database Issue.