Two-phase SSU and SKAT in genetic association studies
Xue, Yuan1,2; Ding, Juan3; Wang, Jinjuan1,4; Zhang, Sanguo1,2; Pan, Dongdong5
AbstractThe 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 lose power 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. By applying 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(-6). These findings suggest that tpSSU and tpSKAT can be effective in identifying genetic variants for complex diseases in case-control association studies.
Keywordmultiple-markers analysis genetic model Hardy-Weinberg equilibrium power
Indexed BySCI
Funding ProjectNational Science Foundation of China[11661080] ; National Science Foundation of China[11501134] ; National Science Foundation of China[11731011] ; University of Chinese Academy of Sciences[Y95401TXX2] ; Ten-thousand Talents Program and Applied Basic Research Projects of Yunnan Province[2017FB002]
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000521230000001
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Document Type期刊论文
Corresponding AuthorPan, Dongdong
Affiliation1.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
2.Chinese Acad Sci, Key Lab Big Data Min & Knowledge Management, Beijing 100049, Peoples R China
3.Guangxi Normal Univ, Sch Math & Stat, Guilin 541004, Peoples R China
4.Chinese Acad Sci, Acad Math & Syst Sci, NCMIS, LSC, Beijing 100190, Peoples R China
5.Yunnan Univ, Yunnan Key Lab Stat Modeling & Data Anal, Kunming 650500, Yunnan, Peoples R China
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GB/T 7714
Xue, Yuan,Ding, Juan,Wang, Jinjuan,et al. Two-phase SSU and SKAT in genetic association studies[J]. JOURNAL OF GENETICS,2020,99(1):10.
APA Xue, Yuan,Ding, Juan,Wang, Jinjuan,Zhang, Sanguo,&Pan, Dongdong.(2020).Two-phase SSU and SKAT in genetic association studies.JOURNAL OF GENETICS,99(1),10.
MLA Xue, Yuan,et al."Two-phase SSU and SKAT in genetic association studies".JOURNAL OF GENETICS 99.1(2020):10.
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