The Correlation Of Methylation Levels Measured Using Illumina 450K And EPIC Beadchips In Blood Samples
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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.
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The mild correlation among first-generation epigenetic clock age gaps could be due to large technical noise in DNA methylation arrays, which limits robustness across datasets.
“This could be due to the large degree of technical noise in DNA methylation arrays152–154, which limits the robustness of applying these models across datasets.”
From Measuring biological age using omics data (2022) · cites this paper as [153]
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References 26 · Cited by 139
- Authors
- Logue, M. W., Smith, A. K., Wolf, E. J., Maniates, H., Stone, A., Schichman, S. A., McGlinchey, R. E., Milberg, W., & Miller, M. W.
- Affiliations
- Boston University (US)
- Emory University (US)
- VA Boston Healthcare System (US)
- Central Arkansas Veterans Healthcare System (US)
- Harvard University (US)
- Corresponding author
- Logue, Mark W
- ORCID
- Venue
- Epigenomics
- Publisher
- Informa UK Limited
- Published
- 2017-08-15
- Volume
- 9
- Issue
- 11
- Pages
- 1363-1371
- ISSN
- 1750-1911 (ISSN-L)
- 1750-192X
- PMC
- PMC5967357
- OpenAlex
- W2745699865
- Cited by
- 139
- References
- 26
- Citations by year
- 2026: 3 · 2025: 9 · 2024: 20 · 2023: 21 · 2022: 16 · 2021: 20 · 2020: 23 · 2019: 11 · 2018: 15 · 2017: 1
- FWCI
- 5.58
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Epigenomics (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- MW Miller owns stock in Illumina, Inc (I01BX003477)
- VA BLR & D grant to MW Logue (1R03AG051877, 1I01CX001276–01A2)
- EJ Wolf (R21MH102834)
- MW Miller (1R01MH108826)
- AK Smith/MW Logue/C Nievergelt/M Uddin and the Translational Research Center for TBI and Stress Disorders (TRACTS)
- VA Rehabilitation Research and Development (RR & D) Traumatic Brain Injury Center of Excellence (B9254-C)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- DNA methylation, Infinium MethylationEPIC BeadChip, whole blood DNA, CpG sites, reproducibility, epigenome-wide association study
- MeSH terms
- Humans, Reproducibility of Results, Biomarkers, Sequence Analysis, DNA, CpG Islands, DNA Methylation, Molecular Diagnostic Techniques
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