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Review of processing and analysis methods for DNA methylation array data

Year: 2013
Type: review
Abstract: The promise of epigenome-wide association studies and cancer-specific somatic DNA methylation changes in improving our understanding of cancer, coupled with the decreasing cost and increasing coverage of DNA methylation microarrays, has brought about a surge in the use of these technologies. Here, we aim to provide both a review of issues encountered in the processing and analysis of array-based DNA methylation data and a summary of the advantages of recent approaches proposed for handling those issues, focusing on approaches publicly available in open-source environments such as R and Bioconductor. We hope that the processing tools and analysis flowchart described herein will facilitate researchers to effectively use these powerful DNA methylation array-based platforms, thereby advancing our understanding of human health and disease.
DOI: 10.1038/bjc.2013.496
Authors: C S Wilhelm-Benartzi, D C Koestler, M R Karagas, J M Flanagan, B C Christensen, K T Kelsey, C J Marsit, E A Houseman, R Brown
Institutions: Ovarian Cancer Action, Imperial College London, Dartmouth College, Brown University, Oregon State University, Institute of Cancer Research
Language: English
Open Access status: hybrid
Estimated APC paid: $5,190
Funders: Cancer Research UK, Ovarian Cancer Action, Breast Cancer Campaign, National Institutes of Health, National Institute of Mental Health, National Cancer Institute, National Institute of Environmental Health Sciences
Awards: The Molecular Epidemiology of Bladder Cancer, G1814890143, Children's Environmental Health & Disease Prevention Research Center at Dartmouth, Non-Melanoma Skin Cancer in New Hampshire, G5130646826, G5656292200, Epigenetics in Neurodevelopment and Mental Health, Patterns of Somatic Gene Alterations in Oral Cancer, G8507756562, The Boston Collaborative Oral Cancer Study
OpenAlex ID: W2085245717
FWCI: 1.567
Cites: 68
Cited by: 201
Related to: 10