Perhaps the greatest initial utility of GWA findings is in the clues they provide for disease etiology, therapeutic targets, and gene function. As noted above, several of these discoveries have suggested etiologic pathways and therapeutic opportunities not previously implicated in the complex diseases with which they are associated, such as the autophagy pathway in inflammatory bowel disease, the complement pathway in macular degeneration, and the HLA-C locus in control of viral load in HIV infection (9). Intriguing potential genetic connections between diseases previously believed to be unrelated—such as the finding that risks of type 2 diabetes, coronary disease, and familial melanoma are all associated with variants near CDKNA2A/B, or that risks of Crohn’s disease and type 1 diabetes are related to variants near PTPN2—suggest new avenues of research in identifying other similarities in etiology, progression, or treatment of these conditions. The not infrequent occurrence of associations in “gene deserts” far from any known genes invites the question of whether studies of disease pathogenesis have been too focused on coding regions of the genome and have missed other important structural and functional clues to ge-nomic regulation.
