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A two-phase procedure for non-normal quantitative trait genetic association study
Zhang, Wei1; Li, Huiyun2; Li, Zhaohai3; Li, Qizhai1
2016-01-28
Source PublicationBMC BIOINFORMATICS
ISSN1471-2105
Volume17Pages:9
AbstractBackground: 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.
KeywordModel selection Quantitative trait genetic association studies Robustness Two-phase procedure
DOI10.1186/s12859-016-0888-x
Language英语
Funding ProjectNational 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 Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS IDWOS:000368875700001
PublisherBIOMED CENTRAL LTD
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/209
Collection系统科学研究所
Corresponding AuthorLi, Huiyun
Affiliation1.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
Recommended Citation
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.
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