Email updates

Keep up to date with the latest news and content from BMC Genetics and BioMed Central.

Open Access Highly Accessed Methodology article

A non-parametric approach for detecting gene-gene interactions associated with age-at-onset outcomes

Ming Li1, Joseph C Gardiner2, Naomi Breslau2, James C Anthony2 and Qing Lu2*

Author Affiliations

1 Division of Biostatistics, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA

2 Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA

For all author emails, please log on.

BMC Genetics 2014, 15:79  doi:10.1186/1471-2156-15-79

Published: 1 July 2014

Abstract

Background

Cox-regression-based methods have been commonly used for the analyses of survival outcomes, such as age-at-disease-onset. These methods generally assume the hazard functions are proportional among various risk groups. However, such an assumption may not be valid in genetic association studies, especially when complex interactions are involved. In addition, genetic association studies commonly adopt case-control designs. Direct use of Cox regression to case-control data may yield biased estimators and incorrect statistical inference.

Results

We propose a non-parametric approach, the weighted Nelson-Aalen (WNA) approach, for detecting genetic variants that are associated with age-dependent outcomes. The proposed approach can be directly applied to prospective cohort studies, and can be easily extended for population-based case-control studies. Moreover, it does not rely on any assumptions of the disease inheritance models, and is able to capture high-order gene-gene interactions. Through simulations, we show the proposed approach outperforms Cox-regression-based methods in various scenarios. We also conduct an empirical study of progression of nicotine dependence by applying the WNA approach to three independent datasets from the Study of Addiction: Genetics and Environment. In the initial dataset, two SNPs, rs6570989 and rs2930357, located in genes GRIK2 and CSMD1, are found to be significantly associated with the progression of nicotine dependence (ND). The joint association is further replicated in two independent datasets. Further analysis suggests that these two genes may interact and be associated with the progression of ND.

Conclusions

As demonstrated by the simulation studies and real data analysis, the proposed approach provides an efficient tool for detecting genetic interactions associated with age-at-onset outcomes.

Keywords:
Weighted Nelson-Aalen; Cox regression; Progression of nicotine dependence; Joint association