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High throughput fluorescent CE-SSCP SNP genotyping
D Gonen1, J Veenstra-VanderWeele, Z Yang
1Laboratory for Developmental Neuroscience, Child and Adolescent Psychiatry, Department of Psychiatry, University of Chicago, MC3077, 5841 S Maryland Avenue, Chicago, Illinois 60637, USA. ed@yoda.bsd.uchi cago.edu
Abstract:
Large numbers of single nucleotide polymorphisms (SNPs) are being identified by several laboratories for the purpose of developing dense genetic maps. Single-strand conformation polymorphism (SSCP) analysis has been widely used as a method for detecting novel sequence variations in PCR products. Differences in migration of single-stranded DNA can be used not only to find mutations, 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 automated single capillary instrument, relatively rapid and low cost CE-SSCP SNP genotyping using currently available technology is feasible for 135 000 genotypes per year. With parallel multiple array capillary electrophoresis, more genotypes per year may be attainable.