Bayesian modelling of multivariate quantitative traits using seemingly unrelated regressions.
We investigate a Bayesian approach to modelling the statistical association between markers at multiple loci and multivariate quantitative traits. In particular, we describe the use of Bayesian Seemingly Unrelated Regressions (SUR) whereby genotypes at the different loci are allowed to have non-simultaneous effects on the phenotypes considered with residuals from each regression assumed correlated. We present results from simulations showing that, under rather general conditions that are likely to hold in real situations, the Bayesian SUR approach has increased probability of selecting the true model compared to univariate analyses. Finally, we apply our methods to data from subjects genotyped for 12 SNPs in the apolipoprotein E (APOE) gene. Phenotypes relate to response to treatment with atorvastatin and include changes in total cholesterol, low-density lipoprotein cholesterol, and triglycerides. Missing genotype data are naturally accommodated in our Bayesian framework by imputing them using a nested haplotype phasing algorithm.
Verzilli
Claudio J
CJ
Department of Epidemiology and Public Health, Imperial College London, London, United Kingdom. c.verzilli@imperial.ac.uk
Stallard
Nigel
N
Whittaker
John C
JC
D000465:Algorithms; D000924:Anticholesteremic Agents / Q000627:therapeutic use; D001057:Apolipoproteins E / Q000235:genetics; D000069059:Atorvastatin; D001499:Bayes Theorem; D002784:Cholesterol / Q000097:blood; D008078:Cholesterol, LDL / Q000097:blood; D003198:Computer Simulation; D005838:Genotype; D006538:Heptanoic Acids / Q000627:therapeutic use; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D015999:Multivariate Analysis; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011758:Pyrroles / Q000627:therapeutic use; D040641:Quantitative Trait Loci / Q000235:genetics*; D012044:Regression Analysis; D018401:Sample Size; D014280:Triglycerides / Q000097:blood
D000924:Anticholesteremic Agents; D001057:Apolipoproteins E; D008078:Cholesterol, LDL; D006538:Heptanoic Acids; D011758:Pyrroles; D014280:Triglycerides; D002784:Cholesterol; D000069059:Atorvastatin