Efficient genome-wide association testing of gene-environment interaction in case-parent trios.
- Authors
- Gauderman, W James; Thomas, Duncan C; Murcray, Cassandra E; Conti, David; Li, Dalin; Lewinger, Juan Pablo
- Year
- 2010
- Journal
- American journal of epidemiology
- PMID
- 20543031
- DOI
- 10.1093/aje/kwq097
- PMCID
- PMC2915477
Complex trait variation is likely to be explained by the combined effects of genes, environmental factors, and gene x environment (G x E) interaction. The authors introduce a novel 2-step method for detecting a G x E interaction in a genome-wide association study (GWAS) of case-parent trios. The method utilizes 2 sources of G x E information in a trio sample to construct a screening step and a testing step. Across a wide range of models, this 2-step procedure provides substantially greater power to detect G x E interaction than a standard test of G x E interaction applied genome-wide. For example, for a disease susceptibility locus with minor allele frequency of 15%, a binary exposure variable with 50% prevalence, and a GWAS scan of 1 million markers in 1,000 case-parent trios, the 2-step method provides 87% power to detect a G x E interaction relative risk of 2.3, as compared with only 25% power using a standard G x E test. The method is easily implemented using standard software. This 2-step scan for G x E interaction is independent of any prior scan that may have been conducted for genetic main effects, and thus has the potential to uncover new genes in a GWAS that have not been previously identified.
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In this knowledge base
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|---|---|---|
| Gene-environment interaction in psychological traits and disorders. | 2011 | 21219196 |
External
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| A robust and adaptive framework for interaction testing in quantitative traits between multiple genetic loci and exposure variables. | Hecker J et al. | — | 2022 | → |
| A robust and adaptive framework for interaction testing in quantitative traits between multiple genetic loci and exposure variables | Hecker J et al. | — | 2021 | — |
| Case-Parent Trio Studies in Cleft Lip and Palate. | Khan MI et al. | — | 2020 | → |
| A Fast and Accurate Method for Genome-wide Scale Phenome-wide G × E Analysis and Its Application to UK Biobank. | Bi W et al. | — | 2019 | → |
| Case-Only Analysis of Gene-Environment Interactions Using Polygenic Risk Scores. | Meisner A et al. | — | 2019 | → |
| Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. | McAllister K et al. | — | 2017 | → |
| Detection of gene-environment interactions in a family-based population using SCAD. | Kim G et al. | — | 2017 | → |
| Leveraging population information in family-based rare variant association analyses of quantitative traits. | Jiang Y et al. | — | 2017 | → |
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| Disease and Polygenic Architecture: Avoid Trio Design and Appropriately Account for Unscreened Control Subjects for Common Disease. | Peyrot WJ et al. | — | 2016 | → |
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| An Interdisciplinary Approach to Studying Gene-Environment Interactions: From Twin Studies to Gene Identification and Back. | Dick DM | — | 2011 | → |
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