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IMGT/HLA


NAR Molecular Biology Database Collection entry number 173
Robinson J., Waller M.J., Marsh S.G.E.
Anthony Nolan Research Institute, London, UK
Contact hladb@ebi.ac.uk

Database Description

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 1600 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 allele reports, alignment tools, submission tools as well as detailed descriptions of the source cells. We encourage feedback from our users and as a result of this we have been able to provide new tools and facilities for the study of HLA sequences. The database provides the basic tools needed to retrieve allele information and to perform sequence alignments and have been updated since the first release. We also 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 have 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.

Recent Developments

The IMGT/HLA database has been expanded to include more intronic sequences for HLA class I genes. The alignment tool has also been updated to include full intereactive genomic alignments for class I sequences.

Acknowledgements

P Parham, Stanford University, USA
P Stoehr, European Bioinformatics Institute, UK

References

1. Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE. Tissue Antigens (2000), 55:280-287
2. Robinson J, Waller MJ, Parham P, Bodmer JG, Marsh SGE. Nucleic Acids Research (2001), 29:210-213
3. Marsh SGE, Robinson J. Reviews in Immunogenetics (2001) 2:518-531
4. Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SGE. Nucleic Acids Research (2003), 31:311-314


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