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Series GSE80261 Query DataSets for GSE80261
Status Public on Apr 13, 2017
Title DNA methylation signature of human fetal alcohol spectrum disorder
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Prenatal alcohol exposure is the leading preventable cause of behavioural and cognitive deficits, which may affect between 2-5% of children in North America. While the underlying mechanisms of alcohol’s effects on development remain relatively unknown, emerging evidence implicates epigenetic mechanisms in mediating the range of symptoms observed in children with Fetal Alcohol Spectrum Disorder (FASD). Thus, we investigated the effects of prenatal alcohol exposure on genome-wide DNA methylation in the NeuroDevNet FASD cohort, the largest cohort of human FASD samples to date. Genome-wide DNA methylation patterns of buccal epithelial cells were analyzed using the Illumina HumanMethylation450 array on a Canadian cohort of 206 children (110 FASD and 96 controls). Genotyping was performed in parallel using the Infinium HumanOmni2.5-Quad v1.0 BeadChip. After correcting for the effects of genetic background, 658 significantly differentially methylated sites between FASD cases and controls remained, with 41 displaying differences in beta greater than 5%. Furthermore, 203 differentially methylated regions containing 2 or more CpGs were also identified, overlapping with 167 different genes. The majority of differentially methylated genes were highly expressed in samples from the Allen Brain Atlas, which showed high correlations with buccal cell DNA methylation patterns. Furthermore, over-representation analysis of the up-methylated genes displayed a significant enrichment for neurodevelopmental processes and diseases, such as anxiety, epilepsy, and autism spectrum disorders. These findings suggest that prenatal alcohol exposure is associated with distinct DNA methylation patterns in children and adolescents, raising the possibility of an epigenetic biomarker of FASD.
Overall design The Illumina Infinium HumanMethylation450 Beadchip was used to analyze human buccal epithelial cells from children from the NeuroDevNet cohort, assesing genome-wide DNA methylation patterns in children with fetal alcohol spectrum disorder (n=110 ) and controls (n=96) to identify a potential DNA methylation signature of FASD.
Contributor(s) Portales-Casamar E, Lussier AA, Jones MJ, MacIsaac JL, Edgar R, Mah SM, Barhdadi A, Provost S, Lemieux-Perreault L, Chudley AE, Dubé M, Reynolds JN, Pavlidis P, Kobor MS
Citation(s) 27358653
Submission date Apr 13, 2016
Last update date Mar 22, 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)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (216)
GSM2122878 C0002_FASD
GSM2122879 C0003_FASD
GSM2122880 C0004_FASD
BioProject PRJNA318420

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
GSE80261_RAW.tar 1.9 Gb (http)(custom) TAR (of IDAT)
GSE80261_unmethylated_and_methylated_signal.txt.gz 825.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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