Database dbSNP

Single-nucleotide polymorphisms (SNP) presentation. FOOTER has recently made available a function that will allow the identification and presentation of known SNPs in the examined promoters. The SNPs are derived from the dbSNP database (12). Though the presence or absence of SNPs in the promoter region(s) does not weight into the FOOTER analysis, it can provide useful information to the user about possible sites that could be affected by a polymorphism. 

The NCBI established the dbSNP database in September 1998 as a central repository for both SNPs and short INDEL polymorphisms. In June 2004 (Build 121) dbSNP contained 19.9 million SNPs. These SNPs collapse into a nonredundant set of 9.9 million SNPs, known as Reference SNPs (RefSNPs). Further information exists on a subset of the 9.9 million RefSNPs 4.5 million are validated, at least in as much as they have been observed more than once, which is a fairly reliable indicator that the SNPs are likely to be real and of relatively high frequency. There are 840,038 that have a know frequency in at least one population. These quantities of SNPs give a very high level of coverage across the genome, with most known exons now within 1 to 2 kb of at least one SNP in the dbSNP database. 

Sherry, S. T, Ward, M., and Sirotkin, K. (1999). dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 9 677-679. 

Sherry ST, Ward MH, Kholodov M et al. dbSNP the NCBI database of genetic variation. Nucleic Acids Rei 2001 29 308-311. 

Although public databases such as dbSNP18 do contain a large number of known SNPs including their gene and positional information, a significant fraction of SNP mentions in scientific text cannot be mapped to dbSNP entries.19... 

This list was assembled using NCBI Entrez SNP, dbSNP BUILD 128. Abbreviations dbSNP rs No, single nucleotide polymorphism database reference cluster number ADRB2, beta-2-adrenergic receptor, surface. 

Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation. URL http //www.ncbi.nlm. nih.gov/SNP/index.html. Uses SNP in the much looser sense of minor genetic variations and includes microsatellite repeats and small insertion/deletion polymorphisms. 

There is one other significant source of SNP validation—the simple observation of an SNP on independent occasions from different individuals. The massive scale of SNP discovery naturally has resulted in the repeated identification of SNPs across different individuals and populations. This determination usually indicates that an SNP is likely to be widely spread in populations and often of higher frequency. These so-called 2-hit SNPs have been identified in dbSNP and provide preliminary validation for approximately 45% of the SNPs in the database. This allows the user to specify 2-hit validation as a minimal requirement in a query of the database. As an aside, the problem of SNP validation is particularly pertinent to the study of nonsynonymous SNPs, as many nonsynonymous SNPs, particularly those that are nonconservative in nature, tend to be single-hit SNPs with no validation information. Attempts to validate these SNPs tend to be prone to failure. 

There is a bewildering range of approaches for searching dbSNP. The database can be searched directly by SNP accession number, submitter, detection method, population studied, publication, or a sequence-based BLAST search. The Entrez SNP... 

There is no doubt that dbSNP has assumed the de facto position of the primary central SNP database. To accommodate this, HGVbase has repeatedly sought to... 

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