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Series GSE50586 Query DataSets for GSE50586
Status Public on Jan 02, 2014
Title Distinct DNA methylation patterns of cognitive impairment and Trisomy 21 in Down Syndrome
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary The presence of an extra whole or part of chromosome 21 in people with Down syndrome (DS) is associated with multiple neurological changes, including pathological aging that often meets the criteria for Alzheimer’s Disease (AD). While the mechanism underlying these changes is unknown, it has been hypothesized that the presence of the amyloid precursor protein (APP) on chromosome 21 may contribute to the phenotype. Genome-wide DNA methylation abnormalities have been shown in neural tissue of patients with AD, and cells may respond to changes in gene dosage with altered DNA methylation. We therefore examined whole-genome DNA methylation in buccal epithelial cells of adults with DS to determine whether patterns of DNA methylation correlated with DS and/or cognitive impairment. In addition we examined DNA methylation at the APP gene itself, to see whether there were changes in DNA methylation in this population. Using the Illumina 450K Human Methylation Array, we examined more than 485,000 CpG sites distributed across the genome in buccal epithelial cells. We found 297 CpGs to be differentially methylated between the groups, including 26 genes that were represented by more than one CpG. In addition, we found 331 probes that were correlated with cognitive function including 23 genes represented by more than one probe. We found no enrichment on chromosome 21 and targeted analysis of the APP gene revealed weak evidence for epigenetic impacts related to the AD phenotype. Overall, our results indicate that both Trisomy 21 and cognitive impairment are associated with distinct patterns of DNA methylation.
Overall design This cohort consist of genomic DNA extracted from 20 buccal swabs, bisulphite converted and hybridized to the Illumina Infinium HumanMethylation450 Beadchip for genome wide DNA methylation profiling.
Contributor(s) Jones MJ, Farre P, McEwen LM, MacIsaac JL, Watt K, Neumann S, Emberly E, Cynader MS, Virji-Babul N, Kobor MS
Citation(s) 24373378
Submission date Sep 04, 2013
Last update date Mar 22, 2019
Contact name Michael S. Kobor
Phone 6048753803
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 (20)
GSM1224032 DS01
GSM1224033 DS02
GSM1224034 DS03
BioProject PRJNA217987

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Supplementary file Size Download File type/resource
GSE50586_RAW.tar 183.1 Mb (http)(custom) TAR
GSE50586_signal_intensities.txt.gz 50.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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