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

Author

Listed:
  • 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)

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.

Suggested Citation

  • Li Yun & O’Connor George T. & Dupuis Josée & Kolaczyk Eric, 2015. "Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(3), pages 265-277, June.
  • Handle: RePEc:bpj:sagmbi:v:14:y:2015:i:3:p:265-277:n:4
    DOI: 10.1515/sagmb-2014-0073
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    References listed on IDEAS

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