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Review of processing and analysis methods for DNA methylation array data

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Title: Review of processing and analysis methods for DNA methylation array data
Authors: Wilhelm-Benartzi, CS
Koestler, DC
Karagas, MR
Flanagan, JM
Christensen, BC
Kelsey, KT
Marsit, CJ
Houseman, EA
Brown, R
Item Type: Journal Article
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.
Issue Date: 27-Aug-2013
Date of Acceptance: 30-Jul-2013
URI: http://hdl.handle.net/10044/1/40818
DOI: http://dx.doi.org/10.1038/bjc.2013.496
ISSN: 1532-1827
Publisher: Cancer Research UK
Start Page: 1394
End Page: 1402
Journal / Book Title: British Journal of Cancer
Volume: 109
Issue: 6
Copyright Statement: This work is licensed under the Creative Commons Attribution-NonCommercial-Share Alike 3.0 Unported License.
Sponsor/Funder: Cancer Research UK
Funder's Grant Number: C536/A13086
Keywords: Science & Technology
Life Sciences & Biomedicine
Oncology
ONCOLOGY
DNA methylation
microarray
processing
analysis
bioconductor and R packages
GENOME-WIDE METHYLATION
SURROGATE VARIABLE ANALYSIS
ILLUMINA INFINIUM PLATFORM
GRAPHICAL USER-INTERFACE
MICROARRAY DATA
DIFFERENTIAL METHYLATION
GENE-EXPRESSION
QUANTILE NORMALIZATION
SUBSET-QUANTILE
R PACKAGE
DNA Methylation
DNA, Neoplasm
Epigenesis, Genetic
Humans
Neoplasms
Oligonucleotide Array Sequence Analysis
Oncology & Carcinogenesis
1112 Oncology And Carcinogenesis
Publication Status: Published
Appears in Collections:Division of Surgery
Division of Cancer
Faculty of Medicine



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