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Title: Whole-genome saliva and blood DNA methylation patterns in individuals with a respiratory allergy      
dateReleased:
01-04-2016
description:
It has been suggested that the etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n=5) compared to healthy controls (n=5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437, respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. Pyrosequencing analysis of 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes, confirmed the absolute levels of methylation as well as the differences between cases and controls as observed from the array data. Our findings show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS to distinguish RA cases from healthy controls. The results were replicated in blood cells of the same individuals and confirmed by selected pyrosequencing analysis. This study provides a proof-of-concept that the analysis of DNA methylation profiles in saliva may offer distinct opportunities for molecular epidemiology studies of RA. Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-73745
refinement:
raw
alternateIdentifiers:
73745
keywords:
functional genomics
dateModified:
01-09-2016
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-GEOD-13534
name:
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482_v.1.1)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-73745/E-GEOD-73745.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-73745/E-GEOD-73745.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73745
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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