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Series GSE39560 Query DataSets for GSE39560
Status Public on May 13, 2013
Title DNA Methylation Profiling of Human Saliva
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Background: Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intrauterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. In a unique cohort of 17 monozygotic (MZ) monochorionic female twins very discordant for birth weight (relative differences ranging from 21.3-35.7%), we examined if adverse prenatal growth conditions experienced by the smaller co-twins lead to systemic long-lasting DNA methylation changes. Genome-wide DNA methylation profiles were acquired from saliva DNA using the Infinium HumanMethylation450 BeadChip, targeting ~2% of all CpGs in the genome.
Results: Overall, co-twins showed very similar genome-wide DNA methylation profiles. Since observed differences were almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3153 were differentially methylated between the heavy and light co-twins at nominal significance (p<0.01), of which 45 showed absolute mean β-value differences >0.05 (max=0.08). Deep bisulfite sequencing of eight such loci revealed that differences remained in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicated no significant intra-pair differences.
Conclusions: Severe intrauterine growth differences observed within these MZ twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.
Overall design DNA methylation profiles of saliva from 17 Adult Female MZ MC Twins discordant for birth weight.
Contributor(s) Souren NY, Lutsik P, Gasparoni G, Tierling S, Gries J, Riemenschneider M, Fryns J, Derom C, Zeegers M, Walter J
Citation(s) 23706164
BioProject PRJNA202225
Submission date Jul 23, 2012
Last update date Mar 22, 2019
Contact name Pavlo Lutsik
Phone 04906813022881
Organization name Saarland University
Lab EpiGenetics
Street address Campus A2.4, 0.04
City Saarbruecken
ZIP/Postal code 66123
Country Germany
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (34)
GSM970888 Saliva Twin pair 1 Twin 1
GSM970889 Saliva Twin pair 1 Twin 2
GSM970890 Saliva Twin pair 2 Twin 1

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
GSE39560_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table

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