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Use of pathway information in molecular epidemiology

Publication ,  Journal Article
Thomas, DC; Conti, DV; Baurley, J; Nijhout, F; Reed, M; Ulrich, CM
Published in: Human Genomics
October 1, 2009

© 2009 Henry Stewart Publications. Candidate gene studies are generally motivated by some form of pathway reasoning in the selection of genes to be studied, but seldom has the logic of the approach been carried through to the analysis. Marginal effects of polymorphisms in the selected genes, and occasionally pairwise gene-gene or gene-environment interactions, are often presented, but a unified approach to modelling the entire pathway has been lacking. In this review, a variety of approaches to this problem is considered, focusing on hypothesis-driven rather than purely exploratory methods. Empirical modelling strategies are based on hierarchical models that allow prior knowledge about the structure of the pathway and the various reactions to be included as 'prior covariates'. By contrast, mechanistic models aim to describe the reactions through a system of differential equations with rate parameters that can vary between individuals, based on their genotypes. Some ways of combining the two approaches are suggested and Bayesian model averaging methods for dealing with uncertainty about the true model form in either framework is discussed. Biomarker measurements can be incorporated into such analyses, and two-phase sampling designs stratified on some combination of disease, genes and exposures can be an efficient way of obtaining data that would be too expensive or difficult to obtain on a full candidate gene sample. The review concludes with some thoughts about potential uses of pathways in genome-wide association studies.

Duke Scholars

Published In

Human Genomics

DOI

EISSN

1479-7364

ISSN

1473-9542

Publication Date

October 1, 2009

Related Subject Headings

  • Genetics & Heredity
 

Citation

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Thomas, D. C., Conti, D. V., Baurley, J., Nijhout, F., Reed, M., & Ulrich, C. M. (2009). Use of pathway information in molecular epidemiology (Accepted). Human Genomics. https://doi.org/10.1186/1479-7364-4-1-21
Thomas, D. C., D. V. Conti, J. Baurley, F. Nijhout, M. Reed, and C. M. Ulrich. “Use of pathway information in molecular epidemiology (Accepted).” Human Genomics, October 1, 2009. https://doi.org/10.1186/1479-7364-4-1-21.
Thomas DC, Conti DV, Baurley J, Nijhout F, Reed M, Ulrich CM. Use of pathway information in molecular epidemiology (Accepted). Human Genomics. 2009 Oct 1;
Thomas, D. C., et al. “Use of pathway information in molecular epidemiology (Accepted).” Human Genomics, Oct. 2009. Scopus, doi:10.1186/1479-7364-4-1-21.
Thomas DC, Conti DV, Baurley J, Nijhout F, Reed M, Ulrich CM. Use of pathway information in molecular epidemiology (Accepted). Human Genomics. 2009 Oct 1;
Journal cover image

Published In

Human Genomics

DOI

EISSN

1479-7364

ISSN

1473-9542

Publication Date

October 1, 2009

Related Subject Headings

  • Genetics & Heredity