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| Status |
Public on Sep 24, 2019 |
| Title |
The PedBE clock estimates DNA methylation age in pediatric buccal cells [dataset 3, GECKO] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| 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.
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| Overall design |
The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation measures in human buccal epithelial swabs from the Gene Expression Collaborative for Kids Only (GECKO, dataset 3, n = 254, age range = 7-12 years) cohort. This cohort is comprised of Canadian children from British Columbia. Buccal epithelial cells were collected with Isohelix DNA buccal swabs using standard collection procedures and stabilized with Isohelix Dri-Capsules for storage at room temperature prior to genomic DNA extraction (Cell Projects Ltd., Kent, UK). Genomic DNA was purified and concentrated using a DNA Clean and Concentrator Kit (Zymo Research, CA, USA).
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| 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(s) |
31611402 |
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| Submission date |
Sep 23, 2019 |
| Last update date |
Dec 19, 2019 |
| Contact name |
Michael S. Kobor |
| Organization name |
Centre for Molecular Medicine and Therapeutics / University of British Columbia
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| Department |
Medical Genetics
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| Lab |
Kobor
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| Street address |
950 West 28th Avenue
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| City |
Vancouver |
| State/province |
BC |
| ZIP/Postal code |
V5Z 4H4 |
| Country |
Canada |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (254)
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| This SubSeries is part of SuperSeries: |
| GSE137503 |
The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells |
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| Relations |
| BioProject |
PRJNA573750 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE137903_RAW.tar |
183.1 Mb |
(http)(custom) |
TAR |
| GSE137903_matrix_processed_GECKO.txt.gz |
502.8 Mb |
(ftp)(http) |
TXT |
| GSE137903_matrix_signal_GECKO.csv.gz |
1.0 Gb |
(ftp)(http) |
CSV |
| Processed data are available on Series record |
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