BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Generation of synthetic data in evaluating interactions for association studies
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
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Large-scale Genome-Wide Association Studies (GWAS) for complex diseases are increasingly common, due to recent advances in genotyping technology. Gene-gene interactions play an important role in the etiology of complex diseases and have to be addressed in GWAS. In this paper, an efficient strategy based on two-stage analysis is proposed. It combines a single-locus approach with a Goodness-Of-Fit (GOF) test in stage one, and selects a promising subset of SNPs to be modelled using a full interaction model in stage two. Extensive simulations using different disease models with different levels of epistasis demonstrate that it achieves higher power than existing approaches.