Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies

Li Yun (), O’Connor George T., Dupuis Josée and Kolaczyk Eric
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Li Yun: Department of Mathematics and Statistics, Boston University, MA 02215, USA Department of Biostatistics, Boston University School of Public Health, MA 02118, USA
O’Connor George T.: Pulmonary Center, Department of Medicine, Boston University School of Medicine, MA 02118, USA
Dupuis Josée: Department of Biostatistics, Boston University School of Public Health, MA 02118, USA
Kolaczyk Eric: Department of Mathematics and Statistics, Boston University, MA 02215, USA

Statistical Applications in Genetics and Molecular Biology, 2015, vol. 14, issue 3, 265-277

Abstract: In genome-wide association studies (GWAS), it is of interest to identify genetic variants associated with phenotypes. For a given phenotype, the associated genetic variants are usually a sparse subset of all possible variants. Traditional Lasso-type estimation methods can therefore be used to detect important genes. But the relationship between genotypes at one variant and a phenotype may be influenced by other variables, such as sex and life style. Hence it is important to be able to incorporate gene-covariate interactions into the sparse regression model. In addition, because there is biological knowledge on the manner in which genes work together in structured groups, it is desirable to incorporate this information as well. In this paper, we present a novel sparse regression methodology for gene-covariate models in association studies that not only allows such interactions but also considers biological group structure. Simulation results show that our method substantially outperforms another method, in which interaction is considered, but group structure is ignored. Application to data on total plasma immunoglobulin E (IgE) concentrations in the Framingham Heart Study (FHS), using sex and smoking status as covariates, yields several potentially interesting gene-covariate interactions.

Keywords: gene-environment/covariate interaction; genome-wide association studies; sparse regression (search for similar items in EconPapers)
Date: 2015
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DOI: 10.1515/sagmb-2014-0073

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