With such a large number of discovered common variants in GWA studies and meta-analyses thereof, one can empirically characterize their features to understand what we have learned and what more we can expect to discover in the future. There has been substantial criticism of GWA studies, and the most commonly cited justification is the inability of discovered SNPs to account for all of the heritability of a disease or trait. On the other hand, proponents of GWA studies cite the numerous novel loci and novel biological mechanisms, which are arising from the study of these traits and diseases in humans. It’s the typical ‘glass half-full or half-empty’ argument. Whether the cost of the GWA experiments that resulted in these biological findings justified the effort is difficult to quantitate, but what is abundantly clear is that the number of novel loci identified from large-scale unbiased association tests of representative common markers across the genome could not have been identified using other approaches such as candidate gene approaches or linkage studies in Mendelian pedigrees. Meta-analysis of GWA datasets has been essential for accomplishing these discoveries.
