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E-GEOD-73745 - Whole-genome saliva and blood DNA methylation patterns in individuals with a respiratory allergy

Status
Released on 4 January 2016, last updated on 9 January 2016
Organism
Homo sapiens
Samples (24)
Array (1)
Protocols (5)
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
Experiment type
methylation profiling by array 
Contacts
Sabine Langie <sabine.langie@vito.be>, Greet Schoeters, Gudrun Koppen, Guy Van Camp, Katarzyna Szarc vel Szic, Ken Declerck, Patrick De Boever, Sabine S Langie, Sophie Traen, Wim Vanden Berghe
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-73745.idf.txt
Sample and data relationshipE-GEOD-73745.sdrf.txt
Raw data (1)E-GEOD-73745.raw.1.zip
Processed data (1)E-GEOD-73745.processed.1.zip
Additional data (1)E-GEOD-73745.additional.1.zip
Array designA-GEOD-13534.adf.txt
Links