Temporal stability and determinants of white blood cell DNA methylation in the breakthrough generations study

James M Flanagan, Mark N Brook, Nick Orr, Katarzyna Tomczyk, Penny Coulson, Olivia Fletcher, Michael E Jones, Minouk J Schoemaker, Alan Ashworth, Anthony J Swerdlow, Robert Brown, Montserrat Garcia-Closas

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

BACKGROUND: Epigenome-wide association studies (EWAS) using measurements of blood DNA methylation are performed to identify associations of methylation changes with environmental and lifestyle exposures and disease risk. However, little is known about the variation of methylation markers in the population and their stability over time, both important factors in the design and interpretation of EWAS. We aimed to identify stable variable methylated probes (VMP), i.e., markers that are variable in the population, yet stable over time.

METHODS: We estimated the intraclass correlation coefficient (ICC) for each probe on the Illumina 450K methylation array in paired samples collected approximately 6 years apart from 92 participants in the Breakthrough Generations Study. We also evaluated relationships with age, reproductive and hormonal history, weight, alcohol intake, and smoking.

RESULTS: Approximately 17% of probes had an ICC > 0.50 and were considered stable VMPs (stable-VMPs). Stable-VMPs were enriched for probes located in "shores" bordering CpG islands, and at approximately 1.3 kb downstream from the transcription start site in the transition between the unmethylated promoter and methylated gene body. Both cross-sectional and longitudinal data analyses provided strong evidence for associations between changes in methylation levels and aging. Smoking-related probes at 2q37.1 and AHRR were stable-VMPs and related to time since quitting. We also observed associations between methylation and weight changes.

CONCLUSION: Our results provide support for the use of white blood cell DNA methylation as a biomarker of exposure in EWAS.

IMPACT: Larger studies, preferably with repeated measures over time, will be required to establish associations between specific probes and exposures.

Original languageEnglish
Pages (from-to)221-9
Number of pages9
JournalCancer Epidemiology Biomarkers & Prevention
Volume24
Issue number1
DOIs
Publication statusPublished - Jan 2015
Externally publishedYes

Keywords

  • Adult
  • Aged
  • Aged, 80 and over
  • DNA Methylation
  • Female
  • Genome-Wide Association Study
  • Humans
  • Leukocytes
  • Male
  • Middle Aged
  • Journal Article
  • Research Support, Non-U.S. Gov't

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  • Cite this

    Flanagan, J. M., Brook, M. N., Orr, N., Tomczyk, K., Coulson, P., Fletcher, O., Jones, M. E., Schoemaker, M. J., Ashworth, A., Swerdlow, A. J., Brown, R., & Garcia-Closas, M. (2015). Temporal stability and determinants of white blood cell DNA methylation in the breakthrough generations study. Cancer Epidemiology Biomarkers & Prevention, 24(1), 221-9. https://doi.org/10.1158/1055-9965.EPI-14-0767