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SBERIA: set-based gene-environment interaction test for rare and common variants in complex diseases
Shuo Jiao1, Li Hsu, Stéphane Bézieau
1Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. sjiao@fhcrc.org
Genetic Epidemiology
|May 31, 2013
Summary
A new set-based gene-environment interaction test (SBERIA) improves power for complex disease studies by aggregating signals. This method identified gene-smoking interactions in colorectal cancer.
Area of Science:
- Genetics
- Epidemiology
- Biostatistics
Background:
- Identifying gene-environment interactions (G × E) is crucial for understanding complex diseases.
- Existing G × E methods often lack power and have few replicated findings.
- Current approaches primarily focus on enhancing power for individual genetic markers.
Purpose of the Study:
- To introduce a novel set-based gene-environment interaction test (SBERIA) to increase statistical power.
- To reduce multiple testing burdens and aggregate signals within genetic marker sets.
- To address challenges in signal aggregation and direction determination within sets.
Main Methods:
- Developed SBERIA, a set-based gene-environment interaction test.
- Utilized correlation screening for G × E to guide genotype aggregation within marker sets.
- Implemented SBERIA within a logistic regression framework, ensuring independence of screening and testing.
Main Results:
- SBERIA demonstrated higher statistical power compared to benchmark methods across various simulation scenarios, including common and rare variants.
- The method maintained correct Type I error rates.
- Applied to genome-wide association studies (GWAS) data, SBERIA revealed significant gene-smoking interactions in colorectal cancer.
Conclusions:
- SBERIA offers a powerful and robust approach for detecting gene-environment interactions in complex diseases.
- The set-based strategy effectively aggregates signals, overcoming limitations of single-marker tests.
- The study provides evidence for gene-smoking interactions influencing colorectal cancer risk.
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