ABSTRACT
Polymerase chain reaction primers must be carefully designed to give specific products from the large and complex human genome. The genomewide methods described above provide clear indications of the presence of a copy-number variation region at a particular location, but less clear information about the precise number of copies of a given sequence. In order to make genomewide association studies as cost-effective as possible, it was necessary to select a subset of all known single nucleotide polymorphism (SNP) for analysis. The extreme technical challenge of simultaneously typing a sufficient number of SNPs to carry out genomewide association studies has been met by a number of microarray-based technologies, collectively and colloquially known as SNP chips. A simple and robust means to analyze a SNP is by primer extension, where a primer is designed to anneal with its 3’ end immediately adjacent to the SNP site, and then extended by one base, complementary to the SNP allele present in the sequence.
