markers such as location and allele frequencies, which allow investigators to select tagSNPs that best capture the common genetic variation in a particular region, or across the genome. HapMap Phase II increased the number of SNPs genotyped in the four populations to ~ 3.2 million 9; phase III extends the information to an additional seven populations but at a limited number of SNPs (http://www.hapmap.org). Due to the relatively small number of individuals genotyped in the HapMap project - 60 unrelated individuals genotyped in each population sample - only relatively common polymorphisms (with frequency > 0.02) can be captured. However, detecting the influence of rare variation underlying common disease through population-based case-control studies - even with 1000s of cases and controls is difficult, unless effect sizes are very large 2.
