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Original Paper

Free Access

A Bayesian Hierarchical Model for Detecting Haplotype-Haplotype and Haplotype-Environment Interactions in Genetic Association Studies

Li J. · Zhang K. · Yi N.

Author affiliations

Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Ala., USA

Corresponding Author

Nengjun Yi

Department of Biostatistics

University of Alabama at Birmingham

Birmingham, AL 35294-0022 (USA)

Tel. +1 205 934 4924, E-Mail nyi@ms.soph.uab.edu

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Hum Hered 2011;71:148–160

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Abstract

Objective: Genetic association studies based on haplotypes are powerful in the discovery and characterization of the genetic basis of complex human diseases. However, statistical methods for detecting haplotype-haplotype and haplotype-environment interactions have not yet been fully developed owing to the difficulties encountered: large numbers of potential haplotypes and unknown haplotype pairs. Furthermore, methods for detecting the association between rare haplotypes and disease have not kept pace with their counterpart of common haplotypes. Methods/Results: We herein propose an efficient and robust method to tackle these problems based on a Bayesian hierarchical generalized linear model. Our model simultaneously fits environmental effects, main effects of numerous common and rare haplotypes, and haplotype-haplotype and haplotype-environment interactions. The key to the approach is the use of a continuous prior distribution on coefficients that favors sparseness in the fitted model and facilitates computation. We develop a fast expectation-maximization algorithm to fit models by estimating posterior modes of coefficients. We incorporate our algorithm into the iteratively weighted least squares for classical generalized linear models as implemented in the R package glm. We evaluate the proposed method and compare its performance to existing methods on extensive simulated data. Conclusion: The results show that the proposed method performs well under all situations and is more powerful than existing approaches.

© 2011 S. Karger AG, Basel


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Article / Publication Details

First-Page Preview
Abstract of Original Paper

Received: September 27, 2010
Accepted: February 03, 2011
Published online: July 20, 2011
Issue release date: July 2011

Number of Print Pages: 13
Number of Figures: 3
Number of Tables: 3

ISSN: 0001-5652 (Print)
eISSN: 1423-0062 (Online)

For additional information: https://www.karger.com/HHE


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