article Open AccessTop 1% cited
Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array
BMC Genomics · 2019 · Vol. 20(1) · pp. 366–366
Georgina Mansell✉(University of Exeter)T.J. Gorrie-Stone(University of Essex)Yanchun Bao(University of Essex)Meena Kumari(University of Essex)Leonard C. Schalkwyk(University of Essex)Jonathan Mill(University of Exeter)Eilís Hannon(University of Exeter)
Abstract
We propose that a significance threshold of P < 9 × 10<sup>- 8</sup> 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.
Epigenetics and DNA MethylationRNA modifications and cancerGenomics and Chromatin DynamicsBiologyDNA methylationDNA microarrayEPICComputational biologyGeneticsMethylationDNABioinformaticsGene
MeSH terms
HumansLinear ModelsCpG IslandsDNA MethylationOligonucleotide Array Sequence AnalysisEpigenesis, GeneticGenome-Wide Association StudyEpigenomics
Funding
- University of Essex
- Directorate for Biological Sciences
- Medical Research Council
- Economic and Social Research Council
Citations
383
FWCI
15.50
field-weighted impact
References
55
Percentile
99%
vs. same field & year
Citations per year
References
DNA methylation age of human tissues and cell types
Genome biology · 2013 · 7,042 citations
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
BMC Bioinformatics · 2010 · 2,270 citations
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Journal of the Royal Statistical Society Series B (Statistical Methodology) · 1995 · 106,483 citations
A data-driven approach to preprocessing Illumina 450K methylation array data
BMC Genomics · 2013 · 1,246 citations
Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population
PLoS Genetics · 2012 · 715 citations
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
Nature Genetics · 2009 · 2,237 citations
DNA methylation arrays as surrogate measures of cell mixture distribution
BMC Bioinformatics · 2012 · 3,416 citations
DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis
The American Journal of Human Genetics · 2016 · 909 citations
Citation Network
How this paper connects to the literature. Drag to explore, click any node to open that paper.