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Series GSE137682 Query DataSets for GSE137682
Status Public on Sep 19, 2019
Title The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells [dataset 8, BIBO]
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.
The BIBO (Dutch abbreviation for Basale Invloeden op Baby Ontwikkleing) is one of the cohorts to develop the PedBE clock.
 
Overall design In the BIBO cohort (dataset 8), 193 mothers and their children have been followed since week 37 of pregnancy. At age 6 DNA was collected with buccal swabs in 148 of the children, which was used to measure DNA methylation with the Illumina EPIC array by the Kobor Lab at UBC in collaboration with Kieran O'Donnell and Michael Meaney at McGill.
 
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
Submission date Sep 18, 2019
Last update date Dec 19, 2019
Contact name Michael S. Kobor
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)
GPL21145 Infinium MethylationEPIC
Samples (152)
GSM4084553 BIBO_6y_genomic DNA [201516320001_R03C01]
GSM4084554 BIBO_6y_genomic DNA [201530460007_R03C01]
GSM4084555 BIBO_6y_genomic DNA [201530440009_R06C01]
This SubSeries is part of SuperSeries:
GSE137503 The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells
Relations
BioProject PRJNA566201

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
GSE137682_GS_BK_controls_bkgd_BetaIntBeadsDetp.txt.gz 408.1 Mb (ftp)(http) TXT
GSE137682_RAW.tar 2.2 Gb (http)(custom) TAR (of IDAT)
Processed data are available on Series record
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