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

Grace Yoon, Yinan Zheng, Zhou Zhang, Haixiang Zhang, Tao Gao, Brian Joyce, Wei Zhang, Weihua Guan, Andrea A. Baccarelli, Wenxin Jiang, Joel Schwartz, Pantel S. Vokonas, Lifang Hou, Lei Liu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Background: Metabolic syndrome has become a major public health challenge worldwide. The association between metabolic syndrome and DNA methylation is of great research interest. Results: We 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. Conclusion: The 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.

Original languageEnglish (US)
Article number156
JournalBMC bioinformatics
Volume18
Issue number1
DOIs
StatePublished - Mar 7 2017

Keywords

  • Bootstrap
  • Elastic net
  • ISIS
  • Metabolic syndrome
  • Methylation
  • Ultra-high dimensional variable selection

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

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