Reliable identification of large numbers of candidate SNPs from public EST data (original) (raw)

Nature Genetics volume 21, pages 323–325 (1999)Cite this article

Abstract

High-resolution genetic analysis of the human genome promises to provide insight into common disease susceptibility. To perform such analysis will require a collection of high-throughput, high-density analysis reagents. We have developed a polymorphism detection system that uses public-domain sequence data. This detection system is called the single nucleotide polymorphism pipeline (SNPpipeline). The analytic core of the SNPpipeline is composed of three components: PHRED, PHRAP and DEMIGLACE. PHRED and PHRAP are components of a sequence analysis suite developed to perform the semi-automated analysis required for large-scale genomes1,2 (provided courtesy of P. Green). Using these informatics tools, which examine redundant raw expressed sequence tag (EST) data, we have identified more than 3,000 candidate single-nucleotide polymorphisms (SNPs). Empiric validation studies of a set of 192 candidates indicate that 82% identify variation in a sample of ten Centre d'Etudes Polymorphism Humain (CEPH) individuals. Our results suggest that existing sequence resources may serve as a valuable source for identifying genetic variation.

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Authors and Affiliations

  1. Laboratory of Population Genetics, NCI, NIH, Bethesda, 20892, Maryland, USA
    Kenneth H. Buetow
  2. Fox Chase Cancer Center, Philadelphia, 19111, Pennsylvania, USA
    Michael N. Edmonson & Anna B. Cassidy

Authors

  1. Kenneth H. Buetow
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  2. Michael N. Edmonson
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  3. Anna B. Cassidy
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Correspondence toKenneth H. Buetow.

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Buetow, K., Edmonson, M. & Cassidy, A. Reliable identification of large numbers of candidate SNPs from public EST data.Nat Genet 21, 323–325 (1999). https://doi.org/10.1038/6851

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