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Series GSE61653 Query DataSets for GSE61653
Status Public on Sep 24, 2014
Title DNA extracted from saliva for methylation studies of psychiatric traits
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary DNA methylation has become increasingly recognized in the etiology of psychiatric disorders. Because brain tissue is not accessible in living humans, epigenetic studies are most often conducted in blood. Saliva is often collected for genotyping studies but is rarely used to examine DNA methylation because the proportion of epithelial cells and leukocytes varies extensively between individuals. The goal of this study was to evaluate whether saliva DNA is informative for studies of psychiatric disorders. Saliva and blood methylation was clearly distinguishable though there was positive correlation overall. There was little correlation in CpG sites within relevant candidate genes. Correlated CpG sites were more likely to occur in areas of low CpG density (i.e. CpG shores and open seas). There was more variability in CpG sites from saliva than blood, which may reflect its heterogeneity. Thus, this study provides a framework for using DNA methylation from saliva and suggests that DNA methylation of saliva may offer distinct opportunities for epidemiological and longitudinal studies of psychiatric traits.
Overall design DNA methylation was assessed in saliva and blood samples from 64 adult African Americans. Both saliva and blood samples were collected from each participant. Saliva was stored in Oragene DNA sample collection kits (DNA Genotek), and blood was collected in EDTA vacuum tubes. DNA was extracted using the Puregene Genomic DNA kit (Invitrogen). DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina). Analyses for tissue-specific DNA patterns were conducted using linear regression adjusted for appropriate covariates, including estimated cellular proportions. The estimated proportion of epithelial cells in saliva DNA ranged from 3-99% (median 26%). In blood, the estimated proportion of lymphocytes ranged from 25-70% (median 48%) and neutrophils ranged from 42-84% (median 58%). Methylation of 68.8% of all CpG sites differed relative to epithelial cell proportion (FDR<.05). Our results provide a framework for methylation studies in DNA extracted from saliva and highlight the importance of controlling for the proportion of epithelial and leukocyte cells. This presents an attractive opportunity for investigators that have already collected salivary DNA for genetic studies of psychiatric traits.
Contributor(s) Smith AK, Kilaru V, Klengel T, Mercer KB, Bradley B, Conneely KN, Ressler KJ, Binder EB
Citation(s) 25355443
Submission date Sep 22, 2014
Last update date Mar 02, 2022
Contact name Alicia Smith
Organization name Emory University
Street address 101 Woodruff Circle
City Atlanta
ZIP/Postal code 30322
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (128)
GSM1509941 SID [B10072]
GSM1509942 SID [B10073]
GSM1509943 SID [B10132]
BioProject PRJNA261780

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
GSE61653_RAW.tar 183.1 Mb (http)(custom) TAR
GSE61653_non-normalized.txt.gz 292.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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