In comparison, the HapMap Phase III project consists of genotypes for ~1.5 million SNPs assayed for samples of individuals from seven additional populations (http://www.hapmap.org). The seven new reference panels include: African ancestry in Southwest USA (ASW), Chinese in metropolitan Denver, Colorado (CHD), Gujarati Indians in Houston, Texas (GIH), Luhya in Webuye, Kenya (LWK), Mexican ancestry in Los Angeles, California (MEX), Maasai in Kinyawa, Kenya (MKK), and Toscans in Italy (TSI). These new panels capture more global variation and provide more choices for a single best reference panel with potentially increased coverage. However, SNP density is less for these seven panels than for the original four reference panels, thereby providing less coverage. Given the eleven HapMap reference panels, an open and important question is which choice of reference panel(s) most increases genomic coverage for a given study sample.
