Review of processing and analysis methods for DNA methylation array data
File(s)
Author(s)
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.
Date Issued
2013-08-27
Date Acceptance
2013-07-30
Citation
British Journal of Cancer, 2013, 109 (6), pp.1394-1402
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
Cancer Research UK
Grant Number
C536/A13086
Subjects
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