Analysis of DNA Methylation Markers for Tissue Identification in Individuals with Different Clinical Phenotypes Rebecca Weeden, Johnisa Walcott, Haley Ecker, Juliette M. Gorson, Deborah S.B.S. Silva Chemistry Department, Hofstra University, Hempstead-NY, 11549, USA Introduction
Results
Identifying a particular tissue is highly important for an investigation. Many studies have demonstrated that some regions in the DNA show different methylation patterns according to the type of tissue being analyzed. However, these genotype-phenotype associations have not been analyzed in individuals with different clinical phenotypes. Because underlying diseases and different clinical conditions can alter DNA methylation levels, it is important to investigate if the clinical phenotype of an individual can alter methylation patterns and if it is necessary to incorporate changes to data interpretation when using this technique for tissue identification in criminal investigations.
Study GSE73745: Whole-genome saliva and blood DNA methylation patterns in individuals with a respiratory allergy. Blood samples - Difference in average % methylation was calculated for controls and patients. Results for the three CpG sites with the highest % methylation difference are shown below. CpG sites
Gene
Difference in average % methylation
p-value
cg09374293
PRMT2
8.9
0.14
cg21461082
PRMT2
9.7
0.23
cg22517527
PRMT2
9.7
0.06
Saliva samples - Difference in average % methylation was calculated for controls and patients. Results for the four CpG sites with the highest % methylation difference are shown below.
Methodology Article review
Selection of CpG sites
Study GSE73745
Bioinformatics
Data analysis
CpG sites
Gene
Difference in average % methylation
p-value
cg09313931
ZC3H12D
6.4
0.15
cg09374293
PRMT2
6.3
0.11
cg15559674
ZC3H12D
6.5
0.26
cg21461082
PRMT2
6.5
0.23
In conclusion, the clinical phenotype did not have any significant effect in the levels of methylation of the analyzed CpG sites.