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

Mansell, Georgina and Gorrie-Stone, Tyler J and Bao, Yanchun and Kumari, Meena and Schalkwyk, Leonard S and Mill, Jonathan and Hannon, Eilis (2019) 'Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array.' BMC Genomics, 20 (1). 366-. ISSN 1471-2164

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Background There has been a steady increase in the number of studies aiming to identify DNA methylation differences associated with complex phenotypes. Many of the challenges of epigenetic epidemiology regarding study design and interpretation have been discussed in detail, however there are analytical concerns that are outstanding and require further exploration. In this study we seek to address three analytical issues. First, we quantify the multiple testing burden and propose a standard statistical significance threshold for identifying DNA methylation sites that are associated with an outcome. Second, we establish whether linear regression, the chosen statistical tool for the majority of studies, is appropriate and whether it is biased by the underlying distribution of DNA methylation data. Finally, we assess the sample size required for adequately powered DNA methylation association studies. Results We quantified DNA methylation in the Understanding Society cohort (n = 1175), a large population based study, using the Illumina EPIC array to assess the statistical properties of DNA methylation association analyses. By simulating null DNA methylation studies, we generated the distribution of p-values expected by chance and calculated the 5% family-wise error for EPIC array studies to be 9 × 10⁻⁸. Next, we tested whether the assumptions of linear regression are violated by DNA methylation data and found that the majority of sites do not satisfy the assumption of normal residuals. Nevertheless, we found no evidence that this bias influences analyses by increasing the likelihood of affected sites to be false positives. Finally, we performed power calculations for EPIC based DNA methylation studies, demonstrating that existing studies with data on ~ 1000 samples are adequately powered to detect small differences at the majority of sites. Conclusion 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.

Item Type: Article
Uncontrolled Keywords: DNA methylation; Epigenome-wide association study (EWAS); Multiple testing; Illumina EPIC array; Power
Divisions: Faculty of Science and Health
Faculty of Social Sciences
Faculty of Science and Health > Life Sciences, School of
Faculty of Science and Health > Mathematical Sciences, Department of
Faculty of Social Sciences > Institute for Social and Economic Research
SWORD Depositor: Elements
Depositing User: Elements
Date Deposited: 12 Aug 2019 08:38
Last Modified: 23 Sep 2022 19:32

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