Calculating DNA Methylation Age Biomarkers

DNA methylation (DNAm) age was calculated successfully for 1,529 participants based on whole blood data measured by utilizing the Illumina Infinium platform from 2011 EPIC/850 K array. The sample size of the main analyses is smaller (n = 843–1,108) because not all participants filled in the psychological questionnaires. We report results for five DNAm age indicators that were estimated with an online calculator¹. The underlying method and R function are described in Horvath (31 (link)). The produced indicators were normalized, as this improves the predictive accuracy and makes the data more comparable to the training data (32 ). The average correlation between the samples and the gold standard was good (r ~ 0.97). In 60.6% of the samples the predicted tissue was correct and sex was always correctly predicted. This information indicates a high precision of the DNAm age predictions.
These DNAm based biomarkers can be broadly categorized into (cell-)intrinsic and extrinsic measures of epigenetic aging (25 (link), 26 (link), 33 (link)).

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Dobewall H., Keltikangas-Järvinen L., Marttila S., Mishra P.P., Saarinen A., Cloninger C.R., Zwir I., Kähönen M., Hurme M., Raitakari O., Lehtimäki T, & Hintsanen M. (2023). The relationship of trait-like compassion with epigenetic aging: The population-based prospective Young Finns Study. Frontiers in Psychiatry, 14, 1018797.

Publication 2023

Infinium platform EPIC/850 K array

Blood Cell Dna biomarkers Dna methylation Gold Methylation Tissue

Corresponding Organization : Finnish Institute for Health and Welfare

Other organizations : University of Helsinki, Tampere University, Fimlab (Finland), Washington University in St. Louis, Universidad de Granada, Tampere University Hospital, University of Turku, Turku University Hospital

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Variable analysis

independent variables

Independent variables not explicitly mentioned.

dependent variables

DNA methylation (DNAm) age indicators
Predicted tissue type
Predicted sex

control variables

Whole blood data measured by utilizing the Illumina Infinium platform from 2011 EPIC/850 K array
Normalization of the produced DNAm age indicators to improve predictive accuracy and make the data more comparable to the training data

positive controls

The average correlation between the samples and the gold standard was good (r ~ 0.97).

negative controls

In 60.6% of the samples the predicted tissue was correct and sex was always correctly predicted, indicating a high precision of the DNAm age predictions.

Annotations

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