Related Experiment Video
Updated: Feb 24, 2026
Sample Preparation to Bioinformatics Analysis of DNA Methylation: Association Strategy for Obesity and Related Trait Studies
Published on: May 6, 2022
The correlation of methylation levels measured using Illumina 450K and EPIC BeadChips in blood samples
Mark W Logue1,2,3,4, Alicia K Smith5,6, Erika J Wolf1,2
1National Center for PTSD, VA Boston Healthcare System, USA.
Aim:
We examined concordance of methylation levels across the Illumina Infinium HumanMethylation450 BeadChip and the Infinium MethylationEPIC BeadChip.
Methods:
We computed the correlation for 145 whole blood DNA samples at each of the 422,524 CpG sites measured by both chips.
Results:
The correlation at some sites was high (up to r = 0.95), but many sites had low correlation (55% had r < 0.20). The low correspondence between 450K and EPIC measured methylation values at many loci was largely due to the low variability in methylation values for the majority of the CpG sites in blood.
Conclusion:
Filtering out probes based on the observed correlation or low variability may increase reproducibility of BeadChip-based epidemiological studies.
