Epidemiology and Public Health, Imperial College London
Doi
Abstract
Large-scale genetic association studies are carried out with the hope of discovering single
nucleotide polymorphisms involved in the etiology of complex diseases. We propose a
coalescent-based model for association mapping which potentially increases the power to
detect disease-susceptibility variants in genetic association studies with case-control and cohort
design. The approach uses Bayesian partition modelling to cluster haplotypes with
similar disease risks by exploiting evolutionary information. We focus on candidate gene
regions and we split the chromosomal region of interest into sub-regions or windows of high
linkage disequilibrium (LD) therein assuming a perfect phylogeny. The haplotype space is
then partitioned into disjoint clusters within which the phenotype-haplotype association is
assumed to be the same. The novelty of our approach consists in the fact that the distance
used for clustering haplotypes has an evolutionary interpretation, as haplotypes are clustered
according to the time to their most recent common mutation. Our approach is fully
Bayesian and we develop Markov Chain Monte Carlo algorithms to sample efficiently over
the space of possible partitions. We have also developed a Bayesian survival regression model
for high-dimension and small sample size settings. We provide a Bayesian variable selection
procedure and shrinkage tool by imposing shrinkage priors on the regression coefficients. We
have developed a computationally efficient optimization algorithm to explore the posterior
surface and find the maximum a posteriori estimates of the regression coefficients. We compare
the performance of the proposed methods in simulation studies and using real datasets
to both single-marker analyses and recently proposed multi-marker methods and show that
our methods perform similarly in localizing the causal allele while yielding lower false positive
rates. Moreover, our methods offer computational advantages over other multi-marker
approaches