High throughput fluorescent CE-SSCP SNP genotyping

Large numbers of single nucleotide polymorphisms (SNPs) are being identifie d by several laboratories for the purpose of developing dense genetic maps. Single-strand conformation polymorphism (SSCP) analysis has been widely us ed as a method for detecting novel sequence variations in PCR products. Dif ferences in migration of single-stranded DNA can be used not only to find m utations, but to genotype SNPs in large sample populations. Using PCR with fluorescent labeling and automated capillary electrophoresis SSCP (CE-SSCP) , we have developed a panel of 15 functional candidate SNPs. With an automa ted single capillary instrument, relatively rapid and low cost CE-SSCP SNP genotyping using currently available technology is feasible for 135 000 gen otypes per year. With parallel multiple array capillary electrophoresis, mo re genotypes per year may be attainable.