Dataset Information

Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis).

ABSTRACT: Background: Commercially available Illumina DNA methylation arrays (HumanMethylation 27K, HumanMethylation450, and MethylationEPIC BeadChip) can be used for comprehensive DNA methylation analyses of not only the human genome but also other mammalian genomes, ranging from those of nonhuman primates to those of rodents. However, practical application of the EPIC array to the crab-eating macaque has not been reported.

Methods: Through bioinformatic analyses involving cross-species comparison and consideration of probe performance, we selected array probes that can be reliably used for the crab-eating macaque genome. A DNA methylation assay using an EPIC array was performed on genomic DNA extracted from the brains of five crab-eating macaques. The obtained DNA methylation data were compared with a publicly available dataset.

Results: Among the 865 918 probes in the EPIC array, a total of 183 509 probes (21.2%) were selected as high-confidence array probes in the crab-eating macaque. Subsequent comparisons revealed that the data from these probes showed good concordance with other DNA methylation datasets of the crab-eating macaque.

Conclusion: The selected high-confidence array probes would be useful for high-throughput DNA methylation assays of the crab-eating macaque.

SUBMITTER: Nakachi Y

PROVIDER: S-EPMC7722662 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis).

Nakachi Yutaka Y Ishii Kazuhiro K Bundo Miki M Masuda Tomoyuki T Iwamoto Kazuya K

Neuropsychopharmacology reports 20201010 4

<h4>Background</h4>Commercially available Illumina DNA methylation arrays (HumanMethylation 27K, HumanMethylation450, and MethylationEPIC BeadChip) can be used for comprehensive DNA methylation analyses of not only the human genome but also other mammalian genomes, ranging from those of nonhuman primates to those of rodents. However, practical application of the EPIC array to the crab-eating macaque has not been reported.<h4>Methods</h4>Through bioinformatic analyses involving cross-species comp ...[more]

PMID: 33037870

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Project description:BackgroundThere 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.ResultsWe 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.ConclusionWe 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.

Dataset Information

Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis).

Publications

Use of the Illumina EPIC methylation array for epigenomic research in the crab-eating macaque (Macaca fascicularis).

Similar Datasets

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