SNP Detection and Allele Frequency Determination by SSCP

Single-strand conformation polymorphism (SSCP) analysis is a sensitive mutation detection system that has been widely used in the field of medical genetics (1 ,2 ). In this method, PCR products are denatured to become single-stranded, and separated by gel electrophoresis under nondenaturing conditions. A single-stranded fragment with a mutation or single nucleotide polymorphism (SNP) has a different conformation from its wild-type counterpart, and these conformational differences result in differing electrophoretic mobility. To identify SNPs at polymorphic sequence-tagged sites (STSs), it is necessary to sequence the STSs in individuals with different genotypes. However, once an SNP sequence is correlated with the corresponding fragment mobility in an SSCP analysis, sequencing may not be necessary for genotyping, because SSCP electrophoresis is highly reproducible (3 ,4 ).