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Abstract
Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.
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Details
1 University of Copenhagen, Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, Copenhagen, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X)
2 University of Copenhagen, Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, Copenhagen, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X); Aalborg University, Department of Health Science and Technology, Aalborg, Denmark (GRID:grid.5117.2) (ISNI:0000 0001 0742 471X)
3 University of Copenhagen, Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, Copenhagen, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X); Copenhagen University Hospital, Department of Cardiology, Rigshospitalet, Copenhagen, Denmark (GRID:grid.4973.9) (ISNI:0000 0004 0646 7373)
4 Rigshospitalet Copenhagen University Hospital, Department of Cardiothoracic Surgery, Copenhagen, Denmark (GRID:grid.475435.4)