Review of processing and analysis methods for DNA methylation array data

Wilhelm-Benartzi, C.S.; Koestler, D.C.; Karagas, M.R.; Flanagan, J.M.; Christensen, B.C.; Kelsey, K.T.; Marsit, C.J.; Houseman, E.A.; Brown, R.

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.

Citation

Wilhelm-Benartzi, C., Koestler, D., Karagas, M., Flanagan, J., Christensen, B., Kelsey, K., …Brown, R. (2013). Review of processing and analysis methods for DNA methylation array data. British Journal of Cancer, 109(6), 1394-1402. https://doi.org/10.1038/bjc.2013.496

• Journal Article Type: Article
• Acceptance Date: Jul 30, 2013
• Online Publication Date: Aug 27, 2013
• Publication Date: Aug 27, 2013
• Deposit Date: Jun 3, 2016
• Publicly Available Date: Jun 16, 2016
• Journal: British Journal of Cancer
• Print ISSN: 0007-0920
• Electronic ISSN: 1532-1827
• Publisher: Springer Nature
• Peer Reviewed: Peer Reviewed
• Volume: 109
• Issue: 6
• Pages: 1394-1402
• DOI: https://doi.org/10.1038/bjc.2013.496
• Public URL: https://durham-repository.worktribe.com/output/1379678