Hierarchical Gene-Proximity Models for Genome-Wide Association Studies

• Activity Number: 221
• Type: Topic Contributed
• Date/Time: Monday, August 4, 2014 : 2:00 PM to 3:50 PM
• Sponsor: Section on Bayesian Statistical Science
• Author(s): Ian Johnston*+ and Timothy Hancock and Hiroshi Mamitsuka and Luis Carvalho
• Companies: Boston University and National ICT Australia, Victoria Research Laboratory and Kyoto University and Boston University
• Keywords: large p small n ; hierarchical Bayes ; Polya-Gamma latent variable

Abstract

Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining weights according to gene lengths and distances from genes to markers. The proposed model uses these weights to define unique prior probabilities of association for markers based on their proximities to genes that are believed to be relevant to the trait of interest. We use an expectation-maximization algorithm in a filtering step to first reduce the dimensionality of the data and then sample from the posterior distribution of the model parameters to estimate posterior probabilities of association for the markers. We offer practical and meaningful guidelines for the selection of the model tuning parameters and propose a pipeline that exploits a singular value decomposition on the raw data to make our model run efficiently on large data sets. We demonstrate the performance of the model in a simulation study and conclude by discussing the results of a case study using a real-world dataset provided by the Wellcome Trust Case Control Consortium.