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Updated: Sep 16, 2025

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies

Published on: May 6, 2022

Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools.

Beryl C Zhuang^1,2,3, Marcia Smiti Jude^1,2,3, Chaini Konwar^1,2,3

¹Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, Canada.

Life Science Alliance

|July 8, 2025

Summary

This summary is machine-generated.

The new Illumina MethylationEPIC v2.0 (EPICv2) array shows high overall agreement with EPICv1, but version differences impact DNA methylation estimates. Accounting for these variations is crucial for accurate research, especially in meta-analyses.

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Area of Science:

Genomics
Epigenetics
Biotechnology

Background:

The Illumina MethylationEPIC v2.0 (EPICv2) array succeeds EPICv1, retaining most probes and adding new ones.
Investigating concordance between EPICv1 and EPICv2 is essential for DNA methylation studies.

Purpose of the Study:

To assess the concordance between Illumina MethylationEPIC v1.0 (EPICv1) and EPICv2 arrays.
To evaluate the impact of EPIC version on DNA methylation variation and estimates.

Main Methods:

DNA methylation profiling was performed on matched blood samples from four adult cohorts using both EPICv1 and EPICv2 arrays.
Concordance and variation analyses were conducted, considering factors like sample relatedness and cell-type composition.

Main Results:

High array-level concordance was observed between EPICv1 and EPICv2, with variable agreement at the individual probe level.
EPIC version significantly contributed to DNA methylation variation, though less than sample relatedness or cell-type composition.
Modest but significant differences in DNA methylation estimates were found between the two versions, regardless of preprocessing methods.

Conclusions:

Differences between EPICv1 and EPICv2 arrays can influence DNA methylation estimates.
Adjusting for EPIC version or analyzing data separately for each version can resolve discordances.
Accounting for EPIC version is critical for harmonizing data in meta-analyses and longitudinal studies.