A likelihood-based method for haplotype association studies of case-control data with genotyping uncertainty

This paper discusses the associations between traits and haplotypes based on Fl (fluorescent intensity) data sets. We consider a clustering algorithm based on mixtures of t distributions to obtain all possible genotypes of each individual (i.e. "GenoSpec-trum"). We then propose a likelihood-based approach that incorporates the genotyping uncertainty to assessing the associations between traits and haplotypes through a haplotype-based logistic regression model. Simulation studies show that our likelihood-based method can reduce the impact induced by genotyping errors.