The TaqMan method for SNP genotyping.

Single nucleotide polymorphisms (SNPs) are common DNA sequence variations that occur at single bases within the genome. SNPs have been instrumental in elucidating the genetic basis of common, complex diseases using genome-wide association studies, candidate gene case-control association studies, and genome-wide linkage analyses. A key to these studies is genotyping of SNPs. Various methods for SNP genotyping have been developed. For a particular genotyping project, the choice of method is dependent on the number of SNPs (n) and the number of DNA samples (m) to be genotyped. For a genome-wide or large-scale project with very high n and small m, the Affymetrix SNP GeneChip and Illumina GoldenGate BeadChips assays are the ideal methods. For a project involving a small number of SNPs (small n) and a large population (high m), the TaqMan assay is the preferred technology as it has high throughput and is highly accurate, precise, time-efficient, and cost-effective. Here, we describe the detailed procedures for TaqMan SNP genotyping assay, including preparation of high-quality DNA samples, the operating protocol, clarification of technical issues, and discussion of several cautionary notes.