ABSTRACT
The completion of the human genome sequencing project,1,2 the completion of the international haplotype mapping project (HapMap Project),3 and the maturation of the use of microarray technology have created an environment where ultra-high throughput single nucleotide polymorphism (SNP) genotyping is now possible.4 Because the high throughput genotyping methods rely on performing thousands of assays in multiplex, having the complete human genome sequence allows one to design probes that are unique in the genome and sets of probes that are not likely to interact with each other. The HapMap Project has contributed to the discovery of over 10 million SNPs in the human genome and has characterized some 3 million SNPs in four populations in Africa, Asia, and Europe. Knowing exactly where the SNPs are in the genome, whether they are common SNPs, and if they are in linkage disequilibrium with their neighbors makes it possible to identify the set of SNPs most useful for a particular project. The use of microarray technology in nucleic acid analysis has matured to the point where the quality of the microarrays is extremely high, the
hybridization protocols are very robust, and the image analysis algorithms are highly sophisticated.5
