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Human Gene Mutation Database (HGMD)

http://www.hgmd.org

Contact   stensonpd@cardiff.ac.uk


Database Description

By Sempember 2002, HGMD contained over 35,000 different mutations from more than 1400 human genes, the majority being single base-pair substitutions. HGMD has been collecting mutation data for approximately 14 years, and the dataset was made publicly available via the internet in April 1996. Since that time, HGMD has grown considerably, new additions being made at a rate exceeding 4000 per annum. HGMD comprises published single base-pair substitutions in coding, regulatory and splicing-relevant regions of human nuclear genes, as well as deletions, duplications, insertions, repeat expansions, combined micro-insertions and deletions ('indels '), and complex rearrangements. The database does not currently include somatic lesions or mitochondrial genome mutations, although hyper- text links have recently been established between HGMD and MITOMAP. Data are accessible via the Internet on a gene-wise basis; every gene has been allocated one page per mutation type, if data of that type are present. Mutations are entered only once to avoid confusion between recurrent and identical-by-descent lesions. This is because reliable discrimination between these two alternatives requires information available only for a very small proportion of known lesions and any unselective collection of mutation reports would have resulted in the inclusion of numerous references with little or no practical or scientific use. All HGMD entries comprise a reference to the first literature report of a mutation (hyper-text linked to Entrez), the associated disease state, gene name, symbol and chromosomal location. Hypertext links are also provided to OMIM, GDB, GenAtlas, the Human Gene Nomenclature Committee, GeneCards and LocusLink for each gene. Links are also provided to mutation maps, which give a graphical representation of the mutation spectrum for a particular gene, and 'reference cDNA sequences' (currently numbering over 1100) for data checking. All mutation entries (except gross and complex lesions) are allocated a unique Accession Number. HGMD also provides a comprehensive list of locus-specific databases available on the internet, which are also accessible via the appropriate gene pages. Data acquisition for HGMD is currently accomplished by a combination of manual and computerised search procedures, scanning in excess of 400 journals on a weekly/monthly basis. Coverage is limited to original published reports although some data are taken from 'Mutation Updates' or review articles. Mutations reported only in abstract form are not generally included. In a collaboration with Springer-Verlag GmbH, in Heidelberg, HGMD has instituted free online submission and electronic publication of human gene mutation data. Future developments will include the completion of flanking data for micro-insertions and splicing mutations, and the introduction of 'genomic reference sequences' to augment the existing cDNA reference sequence data.

Recent Developments

HGMD has recently entered into a licensing agreement with Celera Genomics of Rockville, MD, USA. As part of this agreement, the University of Wales College of Medicine in Cardiff has undertaken to provide Celera with a period of exclusive access to new information added to HGMD. Thus HGMD data will, together with the SNP Reference Database, be made available to subscribers as part of Celera's web-based Discovery System™. The agreement also allows for future collaborations including joint software and database development. After the period of exclusivity, new HGMD data will be made publically available at the Cardiff site. This collaboration with Celera not only guarantees the future of HGMD but will also allow us to greatly improve and expand our service on the public website whilst still maintaining our scientific research programme. Another recent development is the linking of HGMD entries to unpublished mutation data available in online public locus-specific mutation databases. These links have been established in order to provide HGMD users with easy and comprehensive access to both published and unpublished mutation data.

REFERENCES

Krawczak M, Ball EV, Fenton I, Stenson PD, Abeysinghe S, Thomas N, Cooper DN: Human
Gene Mutation Database - a biomedical information and research resource. Human Mutation 15(1):45-51, 2000.

Category   Mutation Databases

Go to the abstract in the NAR Database Issue.

 

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