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A quantitative framework for gene-gene interactions in genome-wide studies Indika Rajapakse and Lue Ping Zhao Fred Hutchinson Cancer Research Center 1100 Fairview Ave N M2-B500 Seattle, WA 98109 Understanding complex genetic diseases requires characterization of the genetic architecture affecting disease susceptibility. This includes identifying genes involved and determining the degree to which they affect disease risk. We have developed a saturated gene-gene interaction model with explicit analytical solutions in a simple mathematical framework. This model can be used to represent all two locus models. Furthermore, we have obtained solutions to a three locus model and extended this mathematical framework to a multiple locus case. The saturated model can be used to identify important interactions as a first step in whole genome-wide data analysis. This will significantly alleviate computational burden, as the model requires only simple algebraic manipulation to obtain solutions.
