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dbSNP Overview

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 100 to 300 bases. 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, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. Once discovered, these polymorphisms could be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions. (Note that dbSNP takes the looser 'variation' definition for SNPs, so there is no requirement or assumption about minimum allele frequency.) The data in dbSNP will be integrated with other NCBI genomic data. As with all NCBI projects, the data in dbSNP will be freely available to the scientific community and made available in a variety of forms.

The database is ready to accept data submissions. dbSNP distinguishes a report of how to assay a SNP from the use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay a SNP will often be accompanied by SNP experiments measuring allele occurence in individuals and populations. Because it is expected that data submissions would typically be done in large batches involving hundreds or thousands of SNPs, a flexible file submission format has been devised (see How To Submit).

Additional web interfaces for form-based submissions, querying, and browsing dbSNP are currently under development.


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