Association tests and estimation of haplotype frequencies and of penetrance-related parameters in a case-control study

This study shows the applicability of our algorithm which tests haplotype and qualitative phenotype association, in a case-control study. Although our algorithm named PENHAPLO is originally developed for analysis of a cohort study, it is shown that PENHAPLO is a useful tool for analysis of case-control studies as well. Simulations confirms that type I errors under hypothesis are accurately estimated. The statistical power for alternative hypothesis calculated using the algorithm is comparable to those analyzed using known-phase data.