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Series GSE27097 Query DataSets for GSE27097
Status Public on Feb 01, 2012
Title Pediatric age-associated DNA methylation
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary DNA methylation (DNAm) plays diverse roles in human biology, but this dynamic epigenetic mark remains far from fully characterized. Although earlier studies uncovered loci that undergo age-associated DNAm changes in adults, little is known about such changes during childhood. Despite profound DNAm plasticity during embryogenesis and early development, monozygotic twins show indistinguishable childhood methylation, suggesting DNAm is highly coordinated during the pediatric period. Here we examine the methylation of 27,578 CpG dinucleotides in peripheral blood DNA from 398 boys, aged 3 to 17 years, and find significant age-associated changes in DNAm at 2,078 loci. We report a deficit of such loci on the X chromosome, a preference for specific nucleotides immediately surrounding the interrogated CpG dinucleotide, and a primary association with developmental and immune ontological functions. These pediatric age-associated loci overlap significantly with those previously identified in adults (p < 0.001) but most of the pediatric loci are unique, suggesting many are childhood-specific. Meta-analysis (n = 1080) with two adult studies reveals that the methylation changes in 29.5% of the age-associated pediatric loci follow a linear pattern from childhood into adulthood; however, we also find a three-fold higher rate of change in children compared with adults and that a higher proportion of lifelong changes are more accurately modeled as a function of logarithmic age. We therefore conclude that DNAm changes occur more rapidly during childhood and are imperfectly accounted for by statistical corrections that are linear in age, further suggesting that future DNAm studies are matched closely for age.
Overall design Age associated DNA methylation was evaluated at each CpG locus using a fixed-effects linear regression model adjusting for BeadChip as a covariate to account for batch effects. Analysis of variance (ANOVA) was conducted for each CpG locus to assess the age affect at each CpG locus which was subsequently corrected for multiple hypotheses using a Benjamini-Hochberg FDR.

* Matrix_AllSampleDetection.txt: Detection P-values for each sample and each loci
* Matrix_AllSampleSignal.txt: Signal for Probe A and Probe B for each sample and each loci
* Matrix_Non-Normalized_AllSampleBeta.txt: Beta values calculated using GenomeStudio v2010.3 Methylation Module 1.8.5 as Signal of Probe B / (Signal of Probe A + Signal of Probe B + 100)
* Matrix_Normalized_AllSampleBetaPrime.txt: Beta Prime values used for analysis calculated from the Probe B and Probe A signals as Beta Prime = Signal of Probe B / (Signal of Probe A + Signal of Probe A)
Contributor(s) Barwick BG, Alisch RS, Chopra P, Satten GA, Conneely KN, Warren ST
Citation(s) 22300631
Submission date Feb 05, 2011
Last update date Jan 02, 2015
Contact name Benjamin G Barwick
Phone (404) 285-2964
Organization name Emory University
Department Hematology and Medical Oncology
Lab Boise and Vertino Labs
Street address 1701 Uppergate Drive WCI 4060C Vertino Lab
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
Platforms (1)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (494)
GSM666345 11299.s1
GSM666350 11094.s1
BioProject PRJNA137453

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
GSE27097_Matrix_AllSampleDetection.txt.gz 3.2 Mb (ftp)(http) TXT
GSE27097_Matrix_AllSampleSignal.txt.gz 69.7 Mb (ftp)(http) TXT
GSE27097_Matrix_Non-Normalized_AllSampleBeta.txt.gz 54.0 Mb (ftp)(http) TXT
GSE27097_Matrix_Normalized_AllSampleBetaPrime.txt.gz 34.8 Mb (ftp)(http) TXT
GSE27097_RAW.tar 5.8 Mb (http)(custom) TAR
Raw data is available on Series record
Processed data included within Sample table
Processed data is available on Series record

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