, Volume 22, Issue 4, pp 519-530

Genomics, mutations and the Internet: The naming and use of parts

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Abstract

Mutations are the source of genetic variation and diversity; by their effect, some are neutral, others are pathogenic. In contemporary genetics, mutations appear at the interface between genomics (structural and functional) and genetics (heredity), where they serve gene discovery and mapping (genomics) and generate challenges to modify their phenotypic effects (medical genetics). Assuming the human genome harbours 80000 transcribed genes each possessing at least 100 different (germline) alleles in a typical population, how then to record and recover data on at least 8 million human alleles? Bioinformatics is the essential resource to create the corresponding accessible digital libraries (genomic and locus-specific mutation databases) for this purpose, a goal to which The HUGO Mutation Database Initiative (Science 279: 10–11, 1998) aspires. Guidelines now exist for naming alleles (Hum Mutat 11: 1–3, 1998). The principles behind the practice are illustrated by PAHdb (http://www.mcgill.ca/pahdb), a prototype locus-specific mutation database (NAR 26: 220–225, 1998), and by prototype genomic mutation databases (HGMD (NAR 26: 285–287, 1998), http://www.uwcm.ac.uk/uwcm/mg/hgmd0.html; the EBI mutation database, http://www2.ebi.ac.uk/mutations/; and OMIM, http://www.ncbi.nlm.nih.gov/Omim.html).