It is now possible to perform association studies on a genome-wide scale [up to 1,000,000 single nucleotide polymorphisms (SNPs)] as a result of improved understanding of the variability of the human genome (e.g. HapMap Project, International HapMap Consortium, 2003) and advances in array technology for multiplex genotyping. GWA studies identify frequent SNPs that are associated with common complex disorders. Association between diseases and SNPs with low minor allele frequencies usually remain undetected since these SNPs are not well represented on currently available arrays. A major difficulty in evaluating the results of GWA studies is the issue of multiple testing. The testing of up to 1,000,000 SNPs for their association with a disease leads to many false positive findings, and it is necessary to correct for multiple testing to achieve the level of genome-wide significance. The level of genome-wide significance depends on the number of SNPs analyzed, and the threshold is approximately 5 × 10−8 for the GWA-chips that are used currently (660,000–1,000,000 SNPs) (Dudbridge and Gusnanto, 2008; Hoggart et al., 2008; Pe'er et al., 2008). This correction method is very
