Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array

We propose that a significance threshold of P < 9 × 10⁻ ⁸ adequately controls the false positive rate for EPIC array DNA methylation studies. Moreover, our results indicate that linear regression is a valid statistical methodology for DNA methylation studies, despite the fact that the data do not always satisfy the assumptions of this test. These findings have implications for epidemiological-based studies of DNA methylation and provide a framework for the interpretation of findings from current and future studies.