The PedBE clock estimates DNA methylation age in pediatric buccal cells [APrON]

The development of current biological markers of aging has primarily focused on adult samples. The epigenetic clock is one promising tool for measuring biological age that shows impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several agerelated phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this crucial gap, we aimed to develop a highly accurate, noninvasive biological measure age specific to pediatric samples by using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032) and the performance was assessed in a separate dataset (n = 689). The DNAm at 94 CpG sites was highly predictive of age in the test cohorts (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs (n = 145) from APrON (Albert Pregnancy Outcomes and Nutrition, Dataset 1) which is a Canadian cohort of pregnant women with 3-year child follow-up. DNA methylation was collected at birth (cord blood) and at age 3 months (buccal epithelial), however, we only included the buccal epithelial data in the current study. Tissue extraction/genomic DNA isolation: Genomic DNA was extracted using the Gentra Puregene Buccal Cell Kit (Qiagen #158845). Bisulfite conversion: genomic DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research).