The cost of genotyping has decreased by a factor of 2000 in the past decade due to the development of reliable, robust, and highly multiplexed genotyping systems (meaning that many genetic markers are genotyped simultaneously) and because of competition between multiple companies. As of this writing in mid-2009, Affymetrix and Illumina are the main suppliers of GWAS genotyping platforms. Each uses different technologies and each has advantages and disadvantages in regard to genotyping accuracy, genomic coverage, ease of use, and total cost. Both platforms genotype a predefined set of SNPs, a crucial reason why cost has decreased. SNPs are genotyped as they are relatively common in the human genome and relatively straight-forward to assay.
