Imputation of missing covariate values in epigenome-wide analysis of DNA methylation data

Chong Wu, Ellen W. Demerath, James S. Pankow, Jan Bressler, Myriam Fornage, Megan L. Grove, Wei Chen, Weihua Guan

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


ABSTRACT: DNA methylation is a widely studied epigenetic mechanism and alterations in methylation patterns may be involved in the development of common diseases. Unlike inherited changes in genetic sequence, variation in site-specific methylation varies by tissue, developmental stage, and disease status, and may be impacted by aging and exposure to environmental factors, such as diet or smoking. These non-genetic factors are typically included in epigenome-wide association studies (EWAS) because they may be confounding factors to the association between methylation and disease. However, missing values in these variables can lead to reduced sample size and decrease the statistical power of EWAS. We propose a site selection and multiple imputation (MI) method to impute missing covariate values and to perform association tests in EWAS. Then, we compare this method to an alternative projection-based method. Through simulations, we show that the MI-based method is slightly conservative, but provides consistent estimates for effect size. We also illustrate these methods with data from the Atherosclerosis Risk in Communities (ARIC) study to carry out an EWAS between methylation levels and smoking status, in which missing cell type compositions and white blood cell counts are imputed.

Original languageEnglish (US)
Pages (from-to)132-139
Number of pages8
Issue number2
StatePublished - Feb 1 2016

Bibliographical note

Publisher Copyright:
© 2016 The Author(s). Published with license by Taylor & Francis Group, LLC.


  • DNA methylation
  • Illumina 450K
  • epigenome-wide association
  • missing data
  • phenotype imputation


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