Review of processing and analysis methods for DNA methylation array data

被引：137

作者：

Wilhelm-Benartzi, C. S. ^{[1
]}

Koestler, D. C. ^{[2
]}

Karagas, M. R. ^{[2
]}

Flanagan, J. M. ^{[1
]}

Christensen, B. C. ^{[2
,3
]}

Kelsey, K. T. ^{[4
,5
]}

Marsit, C. J. ^{[2
,3
]}

Houseman, E. A. ^{[6
]}

Brown, R. ^{[1
,7
]}

机构：

[1] Univ London Imperial Coll Sci Technol & Med, Epigenet Unit, Div Canc, Dept Surg & Canc,Fac Med,Ovarian Canc Act Res Ctr, London W12 0NN, England

[2] Dartmouth Coll, Geisel Sch Med, Sect Biostat & Epidemiol, Hanover, NH 03755 USA

[3] Dartmouth Coll, Geisel Sch Med, Dept Pharmacol & Toxicol, Hanover, NH 03755 USA

[4] Brown Univ, Dept Pathol & Lab Med, Providence, RI 02912 USA

[5] Brown Univ, Dept Epidemiol, Providence, RI 02912 USA

[6] Oregon State Univ, Dept Publ Hlth, Corvallis, OR 97331 USA

[7] Inst Canc Res, Sect Mol Pathol, Sutton, Surrey, England

来源：

BRITISH JOURNAL OF CANCER | 2013年 / 109卷 / 06期

关键词：

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;

D O I：

10.1038/bjc.2013.496

中图分类号：

R73 [肿瘤学];

学科分类号：

100214 ;

摘要：

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.

引用

页码：1394 / 1402

页数：9

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