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.