NCBI Variation Resources

Lon Phan, NCBI

The National Center for Biotechnology Information (NCBI) creates and maintain the dbSNP and dbVar databases that archive, process, display and report information related to germline and somatic variants from multiple species. dbSNP house short (<=50bp) genetic variations that include SNV, small indels, and microsatellites. dbVar house large (>50bp) genomic structural variations that include CNV, large indels, and complex variations. The combined databases have over 2 billion variants from over 300 species, including many agriculturally important plants and animals. The primary roles the databases are to process submissions, archive the data, and distribute it for general use. Each submission is assigned a database accession identifier (ss# in dbSNP or nsv#/esv# in dbVar) based either on flanking invariant sequence or locations asserted on reference sequences. Because these assigned accession numbers are stable and can be cited in publications, they facilitate aggregation of additional information from many diverse organisms. These submissions are then processed to aggregate information from multiple submitters (assign rs# in dbSNP), map and annotated on the latest genome assembly and NCBI Reference Sequences (RefSeqs). The data are also integrated with other NCBI resources including genomic browser, Gene, PubMed, Nucleotide, Protein, BioSample, and BioProject. dbSNP and dbVar data are made available in diverse ways: Entrez searches, study-specific reports, annotation on the genome, Sequence Viewer, and ftp downloads as BED, VCF, and other formats. This presentation will highlight the contents and annotations available in dbSNP and dbVar and NCBI tools for search, display, and retrieval of records.