Current genome-wide association studies include a dense set (>100,000) of experimentally genotyped markers across the genome in thousands of individuals using commercially available chips. One way to fill in the gaps between typed markers is to use genotype or haplotype data from an established reference panel to impute genotypes for markers untyped in the study sample. The HapMap project provides one publicly available source of reference panels [The International HapMap Consortium, 2003; The International HapMap Consortium, 2007]. Phase II of the HapMap project consists of genotypes for >3.1 million single nucleotide polymorphisms (SNPs) assayed for 30 trios of Utah residents with ancestry from Northern and Western Europe (CEU), 45 unrelated Han Chinese in Beijing, China (CHB), 45 unrelated Japanese in Tokyo, Japan (JPT), and 30 trios from the Yoruba ethnic group in Ibadan, Nigeria (YRI), yielding a total of 420 founder chromosomes [The International HapMap Consortium, 2003; The International HapMap Consortium, 2007].
