ArticleJournal of genetics2020
Two-phase SSU and SKAT in genetic association studies.
Article in Journal of genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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1 citing paper in PubMed, 1 citations in OpenAlex.
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5 authors at 4 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The sum of squared score (SSU) and sequence kernel association test (SKAT) are the two good alternative tests for genetic association studies in case-control data. Both SSU and SKAT are derived through assuming a dose-response model between the risk of disease and genotypes. However, in practice, the real genetic mode of inheritance is impossible to know. Thus, these two tests might losepower substantially as shown in simulation results when the genetic model is misspecified. Here, to make both the tests suitable in broad situations, we propose two-phase SSU (tpSSU) and two-phase SKAT (tpSKAT), where the Hardy-Weinberg equilibrium test is adopted to choose the genetic model in the first phase and the SSU and SKAT are constructed corresponding to the selected genetic model in the second phase. We found that both tpSSU and tpSKAT outperformed the original SSU and SKAT in most of our simulation scenarios. Byapplying tpSSU and tpSKAT to the study of type 2 diabetes data, we successfully identified some genes that have direct effects on obesity. Besides, we also detected the significant chromosomal region 10q21.22 in GAW16 rheumatoid arthritis dataset, with P<10
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