Bayesian Model Averaging for the X-Chromosome Inactivation Dilemma in Genetic Association Study

X-chromosome is often excluded from the so called ‘wholegenome’ association studies due to its intrinsic difference between males and females. One particular analytical challenge is the unknown status of X-inactivation, where one of the two X-chromosome variants in females may be randomly selected to be silenced. In the absence of biological evidence in favour of one specific model, we consider a Bayesian model averaging framework that offers a principled way to account for the inherent model uncertainty, providing BMA-based posterior density intervals and Bayes factors. We examine the inferential properties of the proposed methods via extensive simulations and an association study of meconium ileus, an intestinal disease occurring in about twenty percent of Cystic Fibrosis patients. Compared with results previously reported assuming the presence of X-inactivation, we show that the proposed Bayesian methods provide more feature-rich quantities that are useful in practice.