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.
Comments or Questions?
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