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Two-phase SSU and SKAT in genetic association studies
Yuan Xue1, Juan Ding, Jinjuan Wang
1School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China. ddpan@ynu.edu.cn.
Journal of Genetics
|February 25, 2020
Summary
New two-phase methods (tpSSU and tpSKAT) improve genetic association studies by selecting the correct genetic model, outperforming existing tests for complex diseases like type 2 diabetes and rheumatoid arthritis.
Area of Science:
- Genetics
- Statistical Genetics
- Bioinformatics
Background:
- Sum of squared score (SSU) and sequence kernel association test (SKAT) are common genetic association tests.
- These tests assume a specific genetic model, which can lead to reduced power if misspecified.
Purpose of the Study:
- To develop robust genetic association tests that are less sensitive to model misspecification.
- Introduce two-phase SSU (tpSSU) and two-phase SKAT (tpSKAT) to enhance power in genetic association studies.
Main Methods:
- Proposed tpSSU and tpSKAT utilize a two-phase approach.
- Phase one employs the Hardy-Weinberg equilibrium test to select an appropriate genetic model.
- Phase two constructs SSU and SKAT based on the selected model.
Main Results:
- Simulations showed tpSSU and tpSKAT outperformed standard SSU and SKAT in most scenarios.
- Applied tpSSU and tpSKAT identified genes associated with obesity in type 2 diabetes data.
- Detected a significant chromosomal region (10q21.22) in a rheumatoid arthritis dataset.
Conclusions:
- tpSSU and tpSKAT offer improved power and flexibility for genetic association studies.
- These methods are effective in identifying genetic variants for complex diseases in case-control studies.
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