Unique aspects of the GWA method have made these discoveries possible. For example, GWA studies allow the investigator to narrow an association region to a 10–100 kilo-base length of DNA, in contrast to the 5–10 megabases usually detected in familial linkage studies. Because GWA regions typically contain only a few genes, rather than the dozens or hundreds implicated in linkage regions, potentially causative variants can be examined much more rapidly and in greater depth. As noted above, systematic interrogation of the entire genome frees the investigator from reliance on inaccurate prior hypotheses based on incomplete understanding of disease pathogen-esis and genome structure and function. The critical importance of this is illustrated by the fact that many of the associations identified to date, such as CFH in macular degeneration (23) and TCF7L2 in type 2 diabetes (6, 46), have been surprising—the genes were not previously suspected of being related to the disease. Some, such as the strong associations of prostate cancer with SNPs in the 8q24 region (47) and Crohn’s disease with the 5p13 region (34), have been in genomic regions
