Bayesian mixture models for the incorporation of prior knowledge to inform genetic association studies

Brooke L. Fridley, Daniel Serie, Gregory Jenkins, Kristin White, William Bamlet, John D. Potter, Ellen L. Goode

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

In the last decade, numerous genome-wide linkage and association studies of complex diseases have been completed. The critical question remains of how to best use this potentially valuable information to improve study design and statistical analysis in current and future genetic association studies. With genetic effect size for complex diseases being relatively small, the use of all available information is essential to untangle the genetic architecture of complex diseases. One promising approach to incorporating prior knowledge from linkage scans, or other information, is to up- or down-weight P-values resulting from genetic association study in either a frequentist or Bayesian manner. As an alternative to these methods, we propose a fully Bayesian mixture model to incorporate previous knowledge into on-going association analysis. In this approach, both the data and previous information collectively inform the association analysis, in contrast to modifying the association results (P-values) to conform to the prior knowledge. By using a Bayesian framework, one has flexibility in modeling, and is able to comprehensively assess the impact of model specification on posterior inferences. We illustrate the use of this method through a genome-wide linkage study of colorectal cancer, and a genome-wide association study of colorectal polyps.

Original languageEnglish (US)
Pages (from-to)418-426
Number of pages9
JournalGenetic epidemiology
Volume34
Issue number5
DOIs
StatePublished - Jul 2010

Keywords

  • Bayesian
  • Genetic association
  • Linkage
  • Mixture model
  • Prior information

ASJC Scopus subject areas

  • Epidemiology
  • Genetics(clinical)

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