Integrative variable selection via Bayesian model uncertainty

Stat Med. 2013 Dec 10;32(28):4938-53. doi: 10.1002/sim.5888. Epub 2013 Jul 3.


We are interested in developing integrative approaches for variable selection problems that incorporate external knowledge on a set of predictors of interest. In particular, we have developed an integrative Bayesian model uncertainty (iBMU) method, which formally incorporates multiple sources of data via a second-stage probit model on the probability that any predictor is associated with the outcome of interest. Using simulations, we demonstrate that iBMU leads to an increase in power to detect true marginal associations over more commonly used variable selection techniques, such as least absolute shrinkage and selection operator and elastic net. In addition, iBMU leads to a more efficient model search algorithm over the basic BMU method even when the predictor-level covariates are only modestly informative. The increase in power and efficiency of our method becomes more substantial as the predictor-level covariates become more informative. Finally, we demonstrate the power and flexibility of iBMU for integrating both gene structure and functional biomarker information into a candidate gene study investigating over 50 genes in the brain reward system and their role with smoking cessation from the Pharmacogenetics of Nicotine Addiction and Treatment Consortium.

Keywords: Bayes factors; genetic association studies; group variable selection; informative model space prior.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Bayes Theorem*
  • Computer Simulation
  • Humans
  • Models, Statistical*
  • Nicotine / metabolism
  • Polymorphism, Single Nucleotide / genetics
  • Receptors, Nicotinic / genetics
  • Receptors, Nicotinic / metabolism
  • Smoking Cessation / methods
  • Uncertainty*


  • Receptors, Nicotinic
  • Nicotine