Genotyping of triallelic SNPs using TaqMan® PCR

Methods for analysis of single nucleotide polymorphisms (SNP) are well developed. However, most ready-made SNP genotyping kits (e.g., those that use TaqMan® PCR) are based on the assumption that the SNP is biallelic. Thus, most kits are unsuitable for triallelic SNPs. We have experienced difficulty genotyping an SNP using TaqMan® PCR. In the present study, we developed a method of genotyping a triallelic SNP (rs3091244: alleles C, A and T) using TaqMan® PCR. We used 2 different genotyping kits: one for C/A allele genotyping, and one for C/T allele genotyping. The results of these 2 kits were combined to complete the genotyping. The subjects were 320 essentially healthy elderly Japanese. The frequencies of the C, A and T alleles were 0.78, 0.155 and 0.065, respectively. This double-tube method using TaqMan® SNP Genotyping Assays was very accurate and convenient, and it should be useful for genotyping in case-control association studies or linkage studies.