Open AccessEvaluation of the usefulness of saliva for DNA methylation analysis in cohort studies
Author(s) -
Murata Yui,
Fujii Ayaka,
Kanata Sho,
Fujikawa Shinya,
Ikegame Tempei,
Nakachi Yutaka,
Zhao Zhilei,
Jinde Seiichiro,
Kasai Kiyoto,
Bundo Miki,
Iwamoto Kazuya
Publication year - 2019
Publication title -
neuropsychopharmacology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.661
H-Index - 13
ISSN - 2574-173X
DOI - 10.1002/npr2.12075
Subject(s) - dna methylation , saliva , cpg site , methylation , epigenetics , biology , methylated dna immunoprecipitation , illumina methylation assay , genomic dna , dna , microbiology and biotechnology , genetics , gene , gene expression , biochemistry
Epigenetic information such as DNA methylation is a useful biomarker that reflects complex gene‐environmental interaction. Peripheral tissues such as blood and saliva are commonly collected as the source of genomic DNA in cohort studies. Epigenetic studies mainly use blood, while a few studies have addressed the epigenetic characteristics of saliva. Methods The effects of methods for DNA extraction and purification from saliva on DNA methylation were surveyed using Illumina Infinium HumanMethylation450 BeadChip. Using 386 661 probes, DNA methylation differences between blood and saliva from 22 healthy volunteers, and their functional and structural characteristics were examined. CpG sites with DNA methylation levels showing large interindividual variations in blood were evaluated using saliva DNA methylation profiles. Results Genomic DNA prepared by simplified protocol from saliva showed a similar quality DNA methylation profile to that derived from the manufacturer provided protocol. Consistent with previous studies, the DNA methylation profiles of blood and saliva showed high correlations. Blood showed 1,514 hypomethylated and 2099 hypermethylated probes, suggesting source‐dependent DNA methylation patterns. CpG sites with large methylation difference between the two sources were underrepresented in the promoter regions and enriched within gene bodies. CpG sites with large interindividual methylation variations in blood also showed considerable variations in saliva. Conclusion In addition to high correlation in DNA methylation profiles, CpG sites showing large interindividual DNA methylation differences were similar between blood and saliva, ensuring saliva could be a suitable alternative source for genomic DNA in cohort studies. Consideration of source‐dependent DNA methylation differences will, however, be necessary.