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Epigenomics. 2009 Dec;1(2):331-45. doi: 10.2217/epi.09.31.

Methods in DNA methylation profiling.

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  • 1Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA.


Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic patterns and offer a perspective on the ever-expanding literature, which we hope will be useful for investigators who are new to this area. The historical aspects that we cover will be helpful in interpreting this literature and we hope that our discussion of the newest analytical methods will stimulate future progress. We emphasize that no single approach can provide a complete view of the overall methylome, and that combinations of several modalities applied to the same sample set will give the clearest picture. Given the unexpected epigenomic patterns and new biological principles, as well as new disease markers, that have been uncovered in recent studies, it is likely that important discoveries will continue to be made using genome-wide DNA methylation profiling.


CpG island; DNA methylation; bisulfite sequencing; differential methylation hybridization; methylated CpG island recovery assay; methylated DNA immunoprecipitation; methylation profiling; methylation-sensitive SNP chip analysis; next-generation DNA sequencing

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