A two-phase procedure for non-normal quantitative trait genetic association study

doi:10.1186/s12859-016-0888-x

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	A two-phase procedure for non-normal quantitative trait genetic association study
	Zhang, Wei 1; Li, Huiyun 2; Li, Zhaohai 3; Li, Qizhai1
	2016-01-28
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	17 页码:9
摘要	Background: The nonparametric trend test (NPT) is well suitable for identifying the genetic variants associated with quantitative traits when the trait values do not satisfy the normal distribution assumption. If the genetic model, defined according to the mode of inheritance, is known, the NPT derived under the given genetic model is optimal. However, in practice, the genetic model is often unknown beforehand. The NPT derived from an uncorrected model might result in loss of power. When the underlying genetic model is unknown, a robust test is preferred to maintain satisfactory power. Results: We propose a two-phase procedure to handle the uncertainty of the genetic model for non-normal quantitative trait genetic association study. First, a model selection procedure is employed to help choose the genetic model. Then the optimal test derived under the selected model is constructed to test for possible association. To control the type I error rate, we derive the joint distribution of the test statistics developed in the two phases and obtain the proper size. Conclusions: The proposed method is more robust than existing methods through the simulation results and application to gene DNAH9 from the Genetic Analysis Workshop 16 for associated with Anti-cyclic citrullinated peptide antibody further demonstrate its performance.
关键词	Model selection Quantitative trait genetic association studies Robustness Two-phase procedure
DOI	10.1186/s12859-016-0888-x
语种	英语
资助项目	National Science Foundation of China[11371353] ; National Science Foundation of China[61134013] ; Breakthrough Project of Strategic Priority Program of the Chinese Academy of Sciences[XDB13040600]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000368875700001
出版者	BIOMED CENTRAL LTD
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/209
专题	系统科学研究所
通讯作者	Li, Huiyun
作者单位	1.Chinese Acad Sci, Acad Math & Syst Sci, Key Lab Syst Control, Beijing 100190, Peoples R China 2.Beijing Inst Technol, Sch Management & Econ, Beijing 100081, Peoples R China 3.George Washington Univ, Dept Stat, Washington, DC 20052 USA
推荐引用方式 GB/T 7714	Zhang, Wei,Li, Huiyun,Li, Zhaohai,et al. A two-phase procedure for non-normal quantitative trait genetic association study[J]. BMC BIOINFORMATICS,2016,17:9.
APA	Zhang, Wei,Li, Huiyun,Li, Zhaohai,&Li, Qizhai.(2016).A two-phase procedure for non-normal quantitative trait genetic association study.BMC BIOINFORMATICS,17,9.
MLA	Zhang, Wei,et al."A two-phase procedure for non-normal quantitative trait genetic association study".BMC BIOINFORMATICS 17(2016):9.