Gene-environment interaction testing in family-based association studies with phenotypically ascertained samples: a causal inference approach

Department of Biostatistics, Division of Biomedical Informatics, Center for Clinical and Translational Science, University of Kentucky, Lexington, KY 40536, USA.
Biostatistics (Impact Factor: 2.24). 11/2011; 13(3):468-81. DOI: 10.1093/biostatistics/kxr035
Source: PubMed

ABSTRACT We propose a method for testing gene-environment (G × E) interactions on a complex trait in family-based studies in which a phenotypic ascertainment criterion has been imposed. This novel approach employs G-estimation, a semiparametric estimation technique from the causal inference literature, to avoid modeling of the association between the environmental exposure and the phenotype, to gain robustness against unmeasured confounding due to population substructure, and to acknowledge the ascertainment conditions. The proposed test allows for incomplete parental genotypes. It is compared by simulation studies to an analogous conditional likelihood-based approach and to the QBAT-I test, which also invokes the G-estimation principle but ignores ascertainment. We apply our approach to a study of chronic obstructive pulmonary disorder.

  • [Show abstract] [Hide abstract]
    ABSTRACT: The study of gene-environment interactions is an increasingly important aspect of genetic epidemiological investigation. Historically, it has been difficult to study gene-environment interactions using a family-based design for quantitative traits or when parent-offspring trios were incomplete. The QBAT-I provides researchers a tool to estimate and test for a gene-environment interaction in families of arbitrary structure that are sampled without regard to the phenotype of interest, but is vulnerable to inflated type I error if families are ascertained on the basis of the phenotype. In this study, we verified the potential for type I error of the QBAT-I when applied to samples ascertained on a trait of interest. The magnitude of the inflation increases as the main genetic effect increases and as the ascertainment becomes more extreme. We propose an ascertainment-corrected score test that allows the use of the QBAT-I to test for gene-environment interactions in ascertained samples. Our results indicate that the score test and an ad hoc method we propose can often restore the nominal type I error rate, and in cases where complete restoration is not possible, dramatically reduce the inflation of the type I error rate in ascertained samples. Copyright © 2013 John Wiley & Sons, Ltd.
    Statistics in Medicine 01/2014; 33(2). DOI:10.1002/sim.5930 · 2.04 Impact Factor
  • Source
    Human Genetics 08/2012; 131(10):1525-31. DOI:10.1007/s00439-012-1209-8 · 4.52 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Over the past three decades, substantial developments have been made on how to infer the causal effect of an exposure on an outcome, using data from observational studies, with the randomized experiment as the golden standard. These developments have reshaped the paradigm of how to build statistical models, how to adjust for confounding, how to assess direct effects, mediated effects and interactions, and even how to analyze data from randomized experiments. The congruence of random transmission of alleles during meiosis and the randomization in controlled experiments/trials, suggests that genetic studies may lend themselves naturally to a causal analysis. In this contribution, we will reflect on this and motivate, through illustrative examples, where insights from the causal inference literature may help to understand and correct for typical biases in genetic effect estimates.
    Human Genetics 08/2012; 131(10):1665-76. DOI:10.1007/s00439-012-1208-9 · 4.52 Impact Factor