High-Throughput Methods for SNP Genotyping

Single nucleotide polymorphisms (SNPs) are ideal markers for identifying genes associated with complex diseases for two main reasons. Firstly, SNPs are densely located on the human genome at about one SNP per approximately 500–1,000 base pairs. Secondly, a large number of commercial platforms are available for semiautomated or fully automated SNP genotyping. These SNP genotyping platforms serve different purposes since they differ in SNP selection, reaction chemistry, signal detection, throughput, cost, and assay flexibility. This chapter aims to give an overview of some of these platforms by explaining the technologies behind each platform and identifying the best application scenarios for each platform through cross-comparison. The readers may delve into more technical details in the following chapters.