Accurately resolving population structure in a sample is important for both linkage and association studies. Understanding population structure can allow us to use homogenous study groups, thus improving our ability to detect population specific linkage and ensuring that false linkage is not detected because of erroneously assigned allele frequencies. In association studies, differences in population structure between cases and controls can result in high rates of both type I and type II errors [e.g., [1-3]]. When population structure can be resolved, matching between cases and controls can be achieved and one possible confounding factor can be removed.
