Blood-based epigenetic estimators of chronological age in human adults using DNA methylation data from the Illumina MethylationEPIC array

• Published in: BMC genomics 2020-10, Vol.21 (1), p.747-13, Article 747
• Main Authors: Lee, Yunsung, Haftorn, Kristine L, Denault, William R P, Nustad, Haakon E, Page, Christian M, Lyle, Robert, Lee-Ødegård, Sindre, Moen, Gunn-Helen, Prasad, Rashmi B, Groop, Leif C, Sletner, Line, Sommer, Christine, Magnus, Maria C, Gjessing, Håkon K, Harris, Jennifer R, Magnus, Per, Håberg, Siri E, Jugessur, Astanand, Bohlin, Jon
• Format: Article
• Language: English
• Subjects: Accuracy; Adolescent; Adult; Adults; Age; Age related diseases; Aged; Aged, 80 and over; Aging; Aquatic birds; Basic Medicine; Bias; Blood; Child; Chronological age; Clocks; Cohort Studies; CpG Islands; Datasets; Deoxyribonucleic acid; Disease age factors; DNA; DNA Methylation; Epigenesis, Genetic; Epigenetic age; Epigenetic inheritance; Epigenetics; Epigenomics; Female; Gene expression; Genetic aspects; Genetic research; Genetic susceptibility; Genomics; Genotypes; Humans; Identification and classification; Illumina MethylationEPIC BeadChip; Medical and Health Sciences; Medical Genetics; Medicin och hälsovetenskap; Medicinsk genetik; Medicinska och farmaceutiska grundvetenskaper; Methodology; Middle Aged; MoBa; Mortality; Observations; Predictions; Pregnancy; Training; Young Adult
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-020-07168-8

Epigenetic clocks have been recognized for their precise prediction of chronological age, age-related diseases, and all-cause mortality. Existing epigenetic clocks are based on CpGs from the Illumina HumanMethylation450 BeadChip (450 K) which has now been replaced by the latest platform, Illumina MethylationEPIC BeadChip (EPIC). Thus, it remains unclear to what extent EPIC contributes to increased precision and accuracy in the prediction of chronological age. We developed three blood-based epigenetic clocks for human adults using EPIC-based DNA methylation (DNAm) data from the Norwegian Mother, Father and Child Cohort Study (MoBa) and the Gene Expression Omnibus (GEO) public repository: 1) an Adult Blood-based EPIC Clock (ABEC) trained on DNAm data from MoBa (n = 1592, age-span: 19 to 59 years), 2) an extended ABEC (eABEC) trained on DNAm data from MoBa and GEO (n = 2227, age-span: 18 to 88 years), and 3) a common ABEC (cABEC) trained on the same training set as eABEC but restricted to CpGs common to 450 K and EPIC. Our clocks showed high precision (Pearson correlation between chronological and epigenetic age (r) > 0.94) in independent cohorts, including GSE111165 (n = 15), GSE115278 (n = 108), GSE132203 (n = 795), and the Epigenetics in Pregnancy (EPIPREG) study of the STORK Groruddalen Cohort (n = 470). This high precision is unlikely due to the use of EPIC, but rather due to the large sample size of the training set. Our ABECs predicted adults' chronological age precisely in independent cohorts. As EPIC is now the dominant platform for measuring DNAm, these clocks will be useful in further predictions of chronological age, age-related diseases, and mortality.