Epigenome-wide meta-analysis of BMI in nine cohorts: Examining the utility of epigenetically predicted BMI

Whitney L. Do, Dianjianyi Sun, Karlijn Meeks, Pierre Antoine Dugué, Ellen Demerath, Weihua Guan, Shengxu Li, Wei Chen, Roger Milne, Abedowale Adeyemo, Charles Agyemang, Rami Nassir, Jo Ann E. Manson, Aladdin H. Shadyab, Lifang Hou, Steve Horvath, Themistocles L. Assimes, Parveen Bhatti, Kristina M. Jordahl, Andrea A. BaccarelliAlicia K. Smith, Lisa R. Staimez, Aryeh D. Stein, Eric A. Whitsel, K. M.Venkat Narayan, Karen N. Conneely*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


This study sought to examine the association between DNA methylation and body mass index (BMI) and the potential of BMI-associated cytosine-phosphate-guanine (CpG) sites to provide information about metabolic health. We pooled summary statistics from six trans-ethnic epigenome-wide association studies (EWASs) of BMI representing nine cohorts (n = 17,034), replicated these findings in the Women's Health Initiative (WHI, n = 4,822), and developed an epigenetic prediction score of BMI. In the pooled EWASs, 1,265 CpG sites were associated with BMI (p < 1E−7) and 1,238 replicated in the WHI (FDR < 0.05). We performed several stratified analyses to examine whether these associations differed between individuals of European and African descent, as defined by self-reported race/ethnicity. We found that five CpG sites had a significant interaction with BMI by race/ethnicity. To examine the utility of the significant CpG sites in predicting BMI, we used elastic net regression to predict log-normalized BMI in the WHI (80% training/20% testing). This model found that 397 sites could explain 32% of the variance in BMI in the WHI test set. Individuals whose methylome-predicted BMI overestimated their BMI (high epigenetic BMI) had significantly higher glucose and triglycerides and lower HDL cholesterol and LDL cholesterol compared to accurately predicted BMI. Individuals whose methylome-predicted BMI underestimated their BMI (low epigenetic BMI) had significantly higher HDL cholesterol and lower glucose and triglycerides. This study confirmed 553 and identified 685 CpG sites associated with BMI. Participants with high epigenetic BMI had poorer metabolic health, suggesting that the overestimation may be driven in part by cardiometabolic derangements characteristic of metabolic syndrome.

Original languageEnglish (US)
Pages (from-to)273-283
Number of pages11
JournalAmerican journal of human genetics
Issue number2
StatePublished - Feb 2 2023


  • BMI
  • DNA methylation
  • adiposity
  • epigenome-wide association study
  • epigenomics
  • metabolic disease
  • obesity
  • prediction

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics


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