Quality and completeness of SNP databases (original) (raw)

Nature Genetics volume 33, pages 457–458 (2003) Cite this article

Abstract

To address the quality and completeness of single-nucleotide polymorphism (SNP) databases, we resequenced 173 kb (spanning 17 loci) in 150 chromosomes of west African and European ancestry. Over 88% of SNPs in the public (TSC and BAC overlap) and Celera databases were confirmed in independent resequencing. Approximately 45% of all human heterozygosity is attributable to SNPs already available from the two databases, and of SNPs with minor-allele frequencies >10%, more than half are represented.

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Figure 1: Estimated number of all SNPs in the human genome that are already represented in the combined Celera and public SNP databases as a function of minor-allele frequency.

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Acknowledgements

We are grateful to D. Richter for computer support; J. Roy for assistance with database searches; B. Ferrell for the Beni samples; J. Platko, T. Lavery, A. Rachupka, T. Takahashi, G. McDonald and K. Sunter for assistance with DNA sequencing and gel scoring; and M. Daly, J. Mullikin and D. Cutler for comments on the analysis and manuscript.

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Authors and Affiliations

  1. Program in Medical and Population Genetics, Whitehead Institute / MIT Center for Genome Research, One Kendall Square, Cambridge, 02139, Massachusetts, USA
    David E. Reich, Stacey B. Gabriel & David Altshuler
  2. Departments of Genetics and Medicine, Harvard Medical School and Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
    David Altshuler

Authors

  1. David E. Reich
  2. Stacey B. Gabriel
  3. David Altshuler

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Correspondence toDavid E. Reich.

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The authors declare no competing financial interests.

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Reich, D., Gabriel, S. & Altshuler, D. Quality and completeness of SNP databases.Nat Genet 33, 457–458 (2003). https://doi.org/10.1038/ng1133

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