dbSNP and dbVar: The NCBI Databases of Simple and Structural Variation

The National Center for Biotechnology Information (NCBI) creates and maintains databases that archive, process, display and report information related to germline and somatic variants from multiple species. Chief among these databases are the Database of Short Genetic Variations (dbSNP) and the Database of Genomic Structural Variations (dbVar).  This presentation will summarize the current function of dbSNP and dbVAR, highlighting recent improvements.

dbSNP and dbVar represent millions of variants from over 270 species, including many agriculturally important plants and animals.  The primary roles for both databases are to process, archive and distribute submitted data.  Each submission is assigned a database identifier (ss# in dbSNP or nssv#/essv# in dbVar) based on invariant flanking sequence or on asserted reference sequence locations.  Submissions are then processed to calculate their location on NCBI Reference Sequences (RefSeqs).  If more than one submission maps to the same location, the submission records are grouped and assigned a stable public accession (rs# in dbSNP or nsv#/esv# in dbVAR).  Because these assigned accession numbers can be cited in publications, they facilitate aggregation of additional information from many diverse organisms.  Once submitted data are accessioned, they are available through Entrez searches, study-specific reports, annotation on the genome, and ftp downloads.  Since dbSNP and dbVar integrate with many NCBI resources, including Gene, PubMed, Nucleotide, and Genome, dbSNP and dbVAR records can be accessed through the records in these NCBI resources.

Researchers and genetic testers are encouraged to submit their variation data and to cite their submissions in manuscripts and on the web.

Acknowledgments

Work at NCBI is supported by the NIH Intramural Research Program and the National Library of Medicine.