Ultra-high dimensional variable selection with application to normative aging study: DNA methylation and metabolic syndrome

BMC Bioinformatics

Methodology Article

Haixiang Zhang¹  Weihua Guan²  Joel Schwartz³  Andrea A. Baccarelli³  Pantel S. Vokonas⁴  Yinan Zheng⁵  Zhou Zhang⁵  Tao Gao⁵  Brian Joyce⁵  Wei Zhang⁵  Lifang Hou⁵  Lei Liu⁵  Grace Yoon⁶  Wenxin Jiang⁶ 

[1] Center for Applied Mathematics, Tianjin University, 92 Weijin Road, 300072, Tianjin, China;Department of Biostatistics, University of Minnesota, 420 Delaware, 55455, Minneapolis, USA;Department of Environmental Health, Harvard University, 677 Huntington Avenue, 02115, Boston, USA;Department of Preventive Medicine and Epidemiology, Boston University, 801 Massachusetts Avenue, 02118, Boston, USA;Department of Preventive Medicine, Northwestern University, 680 N Lake Shore Drive, 60611, Chicago, USA;Department of Statistics, Northwestern University, 2006 Sheridan Road, 60201, Evanston, USA;

关键词: Ultra-high dimensional variable selection;    ISIS;    elastic net;    Bootstrap;    Metabolic syndrome;    methylation;   

DOI  :  10.1186/s12859-017-1568-1

 received in 2016-05-22, accepted in 2017-02-24,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMetabolic syndrome has become a major public health challenge worldwide. The association between metabolic syndrome and DNA methylation is of great research interest.ResultsWe constructed a binomial model to investigate the association between a metabolic syndrome index and DNA methylation in the Normative Aging Study. We applied the Iterative Sure Independence Screening (ISIS) method with elastic net penalty to DNA methylation levels at 484,548 CpG markers from 659 human subjects, and demonstrated that the screening step in ISIS can significantly improve the performance of the elastic net.ConclusionThe proposed method identifies four CpGs which can be mapped to two biologically relevant and functional genes. Identification of significant CpG markers may potentially have practical implications for disease prevention and treatment.

【 授权许可】

CC BY   
© The Author(s) 2017

【 图 表 】

Fig. 6

12951_2017_303_Article_IEq1.gif

12951_2016_246_Article_IEq3.gif

Fig. 6

Fig. 3

12951_2015_155_Article_IEq75.gif

Fig. 2