Single Nucleotide Polymorphism Mapping Array Assay

Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation present in the human genome, and millions of SNPs have been identified (http://www.ncbi.nlm.nih.gov/SNP/ ). Because of their abundance, even spacing, and stability across the genome, SNPs have significant advantages over other genetic markers (such as restriction fragment length polymorphisms and microsatellite markers) as a basis for highresolution whole genome allelotyping. SNP scoring is easily automated and high-density oligonucleotide arrays have recently been generated to support large-scale high throughput SNP analysis. High-density SNP allele arrays have improved significantly and it is now possible to genotype hundreds of thousands SNP markers using a single SNP array. In this chapter, we will provide a detailed experimental protocol of Affymetrix GeneChip SNP Mapping Array-based whole genome SNP genotyping assay.