dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894 USA
This extract was created in the absence of an abstract.
A key aspect of research in genetics is associating sequence variations with heritable phenotypes. The most common variations are single nucleotide polymorphisms (SNPs), which occur approximately once every 500–1000 bases in a large sample of aligned human sequence. Because SNPs are expected to facilitate large-scale association genetics studies, there has recently been great interest in SNP discovery and detection. In collaboration with the National Human Genome Research Institute (NHGRI), the National Center for Biotechnology Information (NCBI) has established the dbSNP database (http://www.ncbi.nlm.nih.gov/SNP) to serve as a central repository for molecular variation. Designed to serve as a general catalog of molecular variation to supplement GenBank (Benson et al. 1999) database submissions can include a broad range of molecular polymorphisms: single base nucleotide substitutions, short deletion and insertion polymorphisms, microsatellite markers, and polymorphic insertion elements such as retrotransposons.
Although the name dbSNP is a slight misnomer given the variations represented, SNP polymorphisms are the largest class of variation in the database, and the name dbSNP, selected at the request of NHGRI, reflects this fact. For the sake of brevity, we elected to use the term SNP as a shorthand for “variation” in the database notation and documentation (http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=how_to_submit). Thus terms used in the documentation like “submitted SNP” or “reference SNP” refer to all classes of variation in the database and should be regarded as meaning “a submitted report of variation” and “a reference report of variation.” Furthermore, it should be noted that in serving its role as the variation complement to GenBank, dbSNP does not restrict submissions to only neutral polymorphisms. Submissions are welcome on all classes of simple molecular variation, including those that cause rare clinical phenotypes.
Submissions to dbSNP come from a variety of sources including individual laboratories, collaborative polymorphism discovery efforts, large-scale genome sequencing centers, and private industry. The data …
