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Series GSE137495 Query DataSets for GSE137495
Status Public on Sep 17, 2019
Title The PedBE clock estimates DNA methylation age in pediatric buccal cells [APrON]
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary 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.
Overall design 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).
Contributor(s) McEwen LM, O’Donnell KJ, McGill MG, Edgar RD, Jones MJ, MacIsaac JL, Lin DT, Ramadori K, Morin A, Gladish N, Garg E, Unternaehrer E, Pokhvisneva I, Karnani N, Kee MZ, Klengel T, Adler NE, Barr RG, Letourneau N, Giesbrecht GF, Reynolds JN, Czamara D, Armstrong JM, Essex MJ, de Weerth C, Beijers R, Tollenaar MS, Bradley B, Jovanovic T, Ressler KJ, Steiner M, Entringer S, Wadhwa PD, Buss C, Bush NR, Binder EB, Boyce WT, Meaney MJ, Horvath S, Kobor MS
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Sep 16, 2019
Last update date Sep 18, 2019
Contact name Michael S. Kobor
Phone 6048753803
Organization name Centre for Molecular Medicine and Therapeutics / University of British Columbia
Department Medical Genetics
Lab Kobor
Street address 950 West 28th Avenue
City Vancouver
State/province BC
ZIP/Postal code V5Z 4H4
Country Canada
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (145)
GSM4080206 Buccal swab, 100994770128_R03C01
GSM4080207 Buccal swab, 100994770128_R05C01
GSM4080208 Buccal swab, 100994770128_R06C01
This SubSeries is part of SuperSeries:
GSE137503 The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells
BioProject PRJNA565738

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE137495_RAW.tar 183.1 Mb (http)(custom) TAR
GSE137495_matrix_signal_APrON.csv.gz 588.1 Mb (ftp)(http) CSV
Raw data are available on Series record
Processed data included within Sample table

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