Increased correlation between methylation sites in epigenome-wide replication studies: impact on analysis and results

Epigenomics. 2017 Dec;9(12):1489-1502. doi: 10.2217/epi-2017-0073. Epub 2017 Nov 6.


Aim: To show that an increased correlation between CpGs after selection through an epigenome-wide association studies (EWAS) might translate into biased replication results.

Methods: Pairwise correlation coefficients between CpGs selected in two published EWAS, the top hits replication, Bonferroni p-values, Benjamini-Hochberg (BH) false discovery rate (FDR) and directional FDR r-values were calculated in the NINFEA cohort data. Exposures' random permutations were performed to show the empirical p-value distributions.

Results: The average pairwise correlation coefficients between CpGs were enhanced after selection for the replication (e.g., from 0.12 at genome-wide level to 0.26 among the selected CpGs), affecting the empirical p-value distributions and the usual multiple testing control.

Conclusion: Bonferroni and Benjamini-Hochberg FDR are inappropriate for the EWAS replication phase, and methods that account for the underlying correlation need to be used.

Keywords: EWAS; bias; correlation; discovery study; epigenetics; replication study.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bias
  • CpG Islands*
  • DNA Methylation
  • DNA Replication*
  • Epigenomics / methods
  • Epigenomics / standards*
  • Genome, Human
  • Genome-Wide Association Study / methods
  • Genome-Wide Association Study / standards*
  • Humans