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Assuming continuous, normally distributed environmental and categorical genotype variables, the authors compare 6 case-only designs for tests of association in gene-environment interaction. Novel tests modeling the environmental variable as either the response or the predictor and allowing a genetic variable with multiallelic variants are included. The authors show that tests imposing the same genotypic pattern of inheritance perform similarly regardless of whether genotype is the response variable or the predictor variable. The novel tests using the genetic variable as the response variable are advantageous because they are robust to non-normally distributed environmental exposures. Dominance deviance-deviation from additivity in the main or interaction effects-is key to test performance: When it is zero or modest, tests searching for a trend with increasing risk alleles are optimal; when it is large, tests for genotypic effects are optimal. However, the authors show that dominance deviance is attenuated when it is observed at a proxy locus, which is common in genome-wide association studies, so large dominance deviance is likely to be rare. The authors conclude that the trend test is the appropriate tool for large-scale association scans where the true gene-environment interaction model is unknown. The common practice of assuming a dominant pattern of inheritance can cause serious losses of power in the presence of any recessive, or modest dominant, effects.

Original publication

DOI

10.1093/aje/kwp398

Type

Journal article

Journal

Am J Epidemiol

Publication Date

15/02/2010

Volume

171

Pages

498 - 505

Keywords

Environment, Genome, Human, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Lung Neoplasms, Models, Genetic, Models, Statistical, Polymorphism, Genetic, Sample Size