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Gene–Environment Interaction: A Variable Selection Perspective

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Epistasis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2212))

Abstract

Gene–environment interactions have important implications for elucidating the genetic basis of complex diseases beyond the joint function of multiple genetic factors and their interactions (or epistasis). In the past, G × E interactions have been mainly conducted within the framework of genetic association studies. The high dimensionality of G × E interactions, due to the complicated form of environmental effects and the presence of a large number of genetic factors including gene expressions and SNPs, has motivated the recent development of penalized variable selection methods for dissecting G × E interactions, which has been ignored in the majority of published reviews on genetic interaction studies. In this article, we first survey existing studies on both gene–environment and gene–gene interactions. Then, after a brief introduction to the variable selection methods, we review penalization and relevant variable selection methods in marginal and joint paradigms, respectively, under a variety of conceptual models. Discussions on strengths and limitations, as well as computational aspects of the variable selection methods tailored for G × E studies, have also been provided.

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Acknowledgements

We thank the editor and reviewers for their invitation, careful review, and insightful comments, leading to a significant improvement of this article. This study has been partly supported by the National Institutes of Health (CA191383, CA204120), the VA Cooperative Studies Program of the Department of VA, Office of Research and Development, an innovative research award from KSU Johnson Cancer Research Center, and a KSU Faculty Enhancement Award.

Author information

Authors and Affiliations

  1. Department of Statistics, Kansas State University, Manhattan, KS, USA

    Fei Zhou, Xi Lu & Cen Wu

  2. Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA

    Shuangge Ma

  3. Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA

    Jie Ren

Authors
  1. Fei Zhou
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  2. Jie Ren
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  3. Xi Lu
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  4. Shuangge Ma
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  5. Cen Wu
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Corresponding author

Correspondence to Cen Wu .

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Editors and Affiliations

  1. Department of Computer Science, City University of Hong Kong, Kowloon Tong, Hong Kong

    Ka-Chun Wong

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Zhou, F., Ren, J., Lu, X., Ma, S., Wu, C. (2021). Gene–Environment Interaction: A Variable Selection Perspective. In: Wong, KC. (eds) Epistasis. Methods in Molecular Biology, vol 2212. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0947-7_13

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  • DOI: https://doi.org/10.1007/978-1-0716-0947-7_13

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0946-0

  • Online ISBN: 978-1-0716-0947-7

  • eBook Packages: Springer Protocols

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