Because of the complexity of human LD patterns, many questions of interest cannot be addressed analytically. We have described in detail our simulation method, HAPGEN, for generating large samples of case and control data at every HapMap SNP, which mimic the patterns of diversity and LD present in the HapMap data. The software can simulate case data under a single causal disease SNP model for specified genotypic relative risks. We have used the method here to assess the power of various commercially available genotyping chips for case-control genome-wide association studies, but note that it could be utilised to assess other design questions, in the evaluation of analytical methods, and in considering follow-on studies such as resequencing and fine-mapping.
