Review of processing and analysis methods for DNA methylation array data

Wilhelm-Benartzi, Charlotte ORCID: https://orcid.org/0000-0003-4927-6158, Koestler, D. C., Karagas, M. R., Flanagan, J. M., Christensen, B. C., Kelsey, K. T., Marsit, C. J., Houseman, E. A. and Brown, R. 2013. Review of processing and analysis methods for DNA methylation array data. British Journal of Cancer 109 (6) , pp. 1394-1402. 10.1038/bjc.2013.496

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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.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Publisher:	Nature Publishing Group
ISSN:	0007-0920
Date of First Compliant Deposit:	8 December 2016
Last Modified:	06 Jan 2024 03:08
URI:	https://orca.cardiff.ac.uk/id/eprint/96186

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