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bioRxiv · 10.1101/466045

Evaluating DNA methylation age on the Illuminas methylationEPIC BeadChip

Dhingra, R.·Kwee, L. C.·Diaz-Sanchez, D.·Devlin, R. B.·Cascio, W.·Hauser, E. R.·Gregory, S.·Shah, S.·Kraus, W.·Olden, K.·Ward-Caviness, C.
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Abstract

DNA methylation age (DNAm age) has become a widely utilized epigenetic biomarker for the aging process. The Horvath method for determining DNAm age is perhaps the most widely utilized and validated DNA methylation age assessment measure. Horvath DNAm age is calculated based on methylation measurements at 353 loci which were present on Illuminas 450k and 27k DNA methylation microarrays. With the increasing use of the more recently developed Illumina MethylationEPIC (850k) microarray, it is worth revisiting this widely used aging measure to evaluate differences in DNA methylation age estimation based on array design. Of the requisite 353 loci, 17 are missing from the current 850k microarray. Using 17 datasets with 27k, 450k, and/or 850k methylation data, we calculated and compared each samples epigenetic age estimated from all 353 loci required from the Horvath DNAm age calculator (full), and using only the 336 loci present on the 27k, 450k, and 850k arrays (reduced). In 450k/27k data, missing loci caused underestimation of epigenetic age when compared with the full clock. Underestimation of full epigenetic age grew from ages 0 to ~20, remaining stable thereafter (mean= -3.46 y, SD=1.13) years for individuals [≥]20 years. Underestimation of DNAm age by the reduced 450k/27k data was similar to the underestimation observed in the 850k data indicating that array differences in DNAm age estimation are primarily driven by missing probes. Correlations between age and DNAm age were not dependent on missing probes or on array designs and consequently associations between DNAm age and outcomes such as sex remained the same independent of missing probes and probe design. In conclusion, DNAm age estimations are array dependent driven by missing probes between arrays. Though correlations and associations with DNAm age may remain the same, researchers should exercise caution when interpreting results based on absolute differences in DNAm age or when mixing samples assayed on different arrays.\n\nDisclaimerThis paper has been reviewed by the National Health and Environmental Effects Research Laboratory, U.S. EPA, and is approved for publication. Approval does not signify that the contents necessarily reflect the views and policies of the agency, nor does mention of trade names or commercial products constitute endorsement or recommendation for use. The authors declare they have no competing financial interests.

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Dhingra, R., Kwee, L. C., Diaz-Sanchez, D., Devlin, R. B., Cascio, W., Hauser, E. R., Gregory, S., Shah, S., Kraus, W., Olden, K., Ward-Caviness, C.. 2018-11-08. Evaluating DNA methylation age on the Illuminas methylationEPIC BeadChip. https://doi.org/10.1101/466045

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