Two new papers address some of the important issues surrounding the detection of susceptibility loci using genome-wide association studies. Both briefly discuss epistasis or gene-gene interactions. See:
Hirschhorn and Daly (2005) Genome-wide association studies for common diseases and complex traits. Nature Reviews Genetics 6:95-108.
Wang et al. (2005) Genome-wide association studies: theoretical and practical concerns. Nature Reviews Genetics 6:109-118.
We published a paper last year that specifically addresses some of the challenges with detecting, characterizing, and interpreting epistasis in genome-wide association studies. See:
Moore and Ritchie (2004) The challenges of whole-genome approaches to common diseases. JAMA 291(13):1642-3.