DNA methylation as a biomarker in environmental epidemiology

DNA methylation/methylomic signatures hold considerable promise as a biomarker of disease or exposure. There are limitations to consider when interpreting DNA methylation data as a biomarker of disease, including whether the tissue used is an appropriate target tissue, whether the results are likely due to shifts in cell populations rather than a direct epigenetic effect, and whether the study design would lead to DNA methylation changes that postdate the development of disease and are therefore not causal. DNA methylation typically occurs at CpG repeat regions in the genome that are overrepresented in promoter and regulatory areas known as CpG islands. Current methylomic arrays that are commercially available include the 850 K Infinium MethylationEPIC BeadChip array that interrogates ~ 850,000 CpG sites in the genome. Alternative sequencing methods include whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) that allows a more focused analysis of sites. Methods for preprocessing and normalization are discussed as well as calculation of differentially methylated regions and methods to adjust for cell type. We conclude by showcasing studies that exemplify the potential utility of methylation biomarkers in environmental epidemiology studies.