Milling SNPs from EST databases

There is considerable interest in the discovery and characterization of sin gle nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a stra tegy that permits the rapid discovery of SNPs from publicly available expre ssed sequence rag (EST) databases. From a set of ESTs derived from 19 diffe rent cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), withou t de novo sequencing. Through a polymerase-mediated, single-base, primer ex tension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele freque ncies 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 libra ries of cDNAs.