Targeted SNP genotyping using the TaqMan® assay

Abstract

More than 99% of genomic DNA sequence is identical among humans, and not surprisingly, slight variations in sequence can often produce a major effect on phenotype. Sequence variants may also mediate the manner in which humans are susceptible to disease or respond to environmental factors such as bacteria, viruses, toxins, chemicals, drugs, and therapeutic interventions. Single-nucleotide polymorphisms (SNPs) are DNA sequence variations that occur when a single base in the genome sequence can be represented by at least two different nucleotides. In the last decade, numerous SNPs have been identified that explain, at least partially, the genetic architecture of complex diseases such as cancer, diabetes, vascular complications, some forms of mental illness, and a multitude of other disorders. Disease-related SNPs are commonly identified through candidate gene approaches, or more recently, through genome-wide association studies. In either case, findings of association require verification in independent, population-based, study samples, usually consisting of several hundreds/thousands of individuals. A convenient technique to genotype a moderate number of markers in this kind of study is available with the TaqMan® platform (Applied Biosystems; Foster City, CA), which utilizes polymerase chain reaction amplification and allelic discrimination to easily and efficiently generate genotype data in a cost-effective way. Here, we introduce and describe this commonly used technique and include protocols that can be directly used in laboratories aiming to perform moderate- to large-scale genotyping studies.