The Correlation Of Methylation Levels Measured Using Illumina 450K And EPIC Beadchips In Blood Samples

Abstract

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.

Keywords::

• DNA methylation
• HumanMethylation450 BeadChip
• Illumina Infinium
• Infinium MethylationEPIC BeadChip
• intraclass correlation

Disclaimer

The views expressed in this article are those of the authors and do not necessarily reflect the position or policy of the Department of Veterans Affairs, the Department of Defense or the US government.

Financial & competing interests disclosure

MW Miller owns stock in Illumina, Inc. This work was funded by I01BX003477, a VA BLR & D grant to MW Logue, 1R03AG051877 and 1I01CX001276–01A2 to EJ Wolf, R21MH102834 to MW Miller, 1R01MH108826 to AK Smith/MW Logue/C Nievergelt/M Uddin and the Translational Research Center for TBI and Stress Disorders (TRACTS), a VA Rehabilitation Research and Development (RR & D) Traumatic Brain Injury Center of Excellence (B9254-C) at VA Boston Healthcare System. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

MW Miller owns stock in Illumina, Inc. This work was funded by I01BX003477, a VA BLR & D grant to MW Logue, 1R03AG051877 and 1I01CX001276–01A2 to EJ Wolf, R21MH102834 to MW Miller, 1R01MH108826 to AK Smith/MW Logue/C Nievergelt/M Uddin and the Translational Research Center for TBI and Stress Disorders (TRACTS), a VA Rehabilitation Research and Development (RR & D) Traumatic Brain Injury Center of Excellence (B9254-C) at VA Boston Healthcare System. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.