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Vol. 9, Issue 2, 167-174, February 1999

METHODS
Mining SNPs From EST Databases

Leslie Picoult-Newberg,1,3 Trey E. Ideker,2 Mark G. Pohl,1 Scott L. Taylor,2 Miriam A. Donaldson,1 Deborah A. Nickerson,2 and Michael Boyce-Jacino1

1 Orchid Biocomputer, Inc., Alpha Center; Johns Hopkins Bayview Research Campus, Baltimore, Maryland 21224 USA; 2 Department of Molecular Biotechnology, University of Washington, Seattle, Washington 98195 USA

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.

[The SNPs identified in this study can be found in the National Center of Biotechnology (NCBI) SNP database under submitter handles ORCHID (SNPS-981210-A) and debnick (SNPS-981209-A and SNPS-981209-B).]

3   Corresponding author.

9:167-174 ©1999 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/99 $5.00
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