The big question is whether we will be able to detect such small effects reliably. There is reason for optimism as the dust begins to settle from the initial GWA explosion. For example, GWA studies have so far used microarrays with one, three or five hundred thousand SNPs; new microarrays are now available with one million SNPs, thus providing greater coverage of the genome. In addition, these microarrays include one million non-polymorphic probes useful for detecting copy number variation mentioned earlier. Even for SNPs, the focus has been on common variants in which the minor allele has a frequency of at least 1%. Most SNPs are less common and such rare SNPs and other types of rare polymorphisms may cumulatively contribute to heritability, although obtaining power to detect rare polymorphisms will be challenging (Bearden, Glahn, Lee, Chiang, van Erp et al., 2008; Ji, Foo, O’Roak, Zhao, Larson et al., 2008)
