Pathway-based association study of multiple candidate genes and multiple traits using structural equation models

Genet Epidemiol. 2015 Feb;39(2):101-13. doi: 10.1002/gepi.21872. Epub 2014 Dec 30.


There is increasing interest in the joint analysis of multiple genetic variants from multiple genes and multiple correlated quantitative traits in association studies. The classical approach involves testing univariate associations between genotypes and phenotypes and correcting for multiple testing that results in loss of power to detect associations. In this paper, we propose modeling complex relationships between genetic variants in candidate genes and measured correlated traits using structural equation models (SEM), taking advantage of prior knowledge on clinical and genetic pathways. We adopt generalized structured component analysis (GSCA) as an approach to SEM and develop a single association test between multiple genetic variants in a gene and a set of correlated traits, taking into account all available data from other genes and other traits. The performance of this test is investigated by simulations. We apply the proposed method to the Quebec Child and Adolescent Health and Social Survey (1999) data to investigate genetic associations with cardiovascular disease-related traits.

Keywords: clinical pathway; generalized structured component analysis; genetic pathway; permutation test; prior biological knowledge.

MeSH terms

  • Adolescent
  • Child
  • Computer Simulation
  • Female
  • Gene Regulatory Networks / genetics*
  • Genes*
  • Genetic Association Studies / methods*
  • Genotype
  • Health Surveys
  • Humans
  • Male
  • Models, Genetic*
  • Phenotype*
  • Polymorphism, Single Nucleotide / genetics*
  • Quebec