Haplotype analysis of case-control data using haplologit: New features

In haplotype-association studies, the risk of a disease is often determined not only by the presence of certain haplotypes but also by their interactions with various environmental factors. The detection of such interactions with case-control data is a challenging task and often requires very large samples. This prompted the development of more efficient estimation methods for analyzing case-control genetic data. The haplologit command implements efficient semiparametric methods, recently proposed in the literature, for fitting haplotype-environment models in the very important special cases of 1) a rare disease, 2) a single candidate gene in Hardy-Weinberg equilibrium, and 3) independence of genetic and environmental factors. In this presentation, I will describe new features of the haplologit command.