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dbSNP: the NCBI database of genetic variation

dbSNP: the NCBI database of genetic variation. S. T. Sherry, M.H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski and K. Sirotkin, Nucleic Acids Research , 29:1, 2001 National Center for Biotechnology Information, National Library of Medicine, National Institute of Health

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dbSNP: the NCBI database of genetic variation

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  1. dbSNP: the NCBI database of genetic variation S. T. Sherry, M.H. Ward, M. Kholodov, J. Baker, L. Phan, E. M. Smigielski and K. Sirotkin, Nucleic Acids Research, 29:1, 2001 National Center for Biotechnology Information, National Library of Medicine, National Institute of Health http://www.ncbi.nlm.nih.gov/SNP

  2. Composition of SNP database • Scope: • Disease-causing mutations • Neutral polymorphisms • Sequence info around polymorphism • Experimental conditions • Population description • Frequency

  3. A Link to other resources • Provides information for searches that start in other resources • LinkOut URLs are external databases that extend beyond NCBI • Phenotypic results are available through external databases

  4. Submission Required info: • Contact information of submitter • Alleles at locus • Flanking sequence surrounding polymorphism • Experimental methods • GenBank record • Population sample and source organism • Frequency data * Major contributors to the database are laboratories associated with the  National Human Genome Research Institute (NHGRI) grants program

  5. After Submission • ss#: dbSNP accessioning to each submitted variation • rs#: Unique variation in an organism reference genome

  6. NCBI resources Gene name Map location BLAST dbSNP Accession number Submitter name Local batch ID Method of identification Population type Publication title Chromosome report Searching the database

  7. Brief summary of Scale • 24 different species have SNP data, including, H. sapiens, A. gambiae, • C. elegans, P. falciparum, Z. mays • 13 million submissions for H. sapiens • 1.4 million in A. gambiae • 2.8 millions new submission for H. sapiens * A total of only 5 species and 1.5 million submissions were present in 2001, at time of publishing

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