How many SNPs should be tested? Studies of small regions revealed LD blocks within which common SNPs are highly correlated (usually less than 10-30,000 bp in Africans, or 30-50,000 in the newer European or Asian populations).(22) This motivated the HapMap project (www.hapmap.org) (12), which has validated around 4 million SNPs including 2.8 million of the estimated 10 million common SNPs in major world populations, while creating competition among biotechnology companies to develop high-throughput genotyping technologies. Sequencing and genotyping studies showed that sets of 500,000 (Europeans) to 1,000,000 (Africans) SNPs could “tag” (serve as proxies for) around 80% of common SNPs. (23) Over the last three years, the Affymetrix and Illumina companies have developed ”chips” (arrays of assays on glass slides) that assay large SNP sets with high accuracy (0-2% missing data, less than 0.5% errors), at low cost (around US$500 per subject, around a 2000-fold reduction in cost per genotype in ten years) and rapidly (over 1,000 DNA specimens per week in some labs). The GWAS era has arrived.
