The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Quantitative comparison of genome-wide DNA methylation mapping technologies
Open accessAbstract
DNA methylation plays a key role in regulating eukaryotic gene expression. Although mitotically heritable and stable over time, patterns of DNA methylation frequently change in response to cell differentiation, disease and environmental influences. Several methods have been developed to map DNA methylation on a genomic scale. Here, we benchmark four of these approaches by analyzing two human embryonic stem cell lines derived from genetically unrelated embryos and a matched pair of colon tumor and adjacent normal colon tissue obtained from the same donor. Our analysis reveals that methylated DNA immunoprecipitation sequencing (MeDIP-seq), methylated DNA capture by affinity purification (MethylCap-seq), reduced representation bisulfite sequencing (RRBS) and the Infinium HumanMethylation27 assay all produce accurate DNA methylation data. However, these methods differ in their ability to detect differentially methylated regions between pairs of samples. We highlight strengths and weaknesses of the four methods and give practical recommendations for the design of epigenomic case-control studies.
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Cites
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Finding the missing heritability of complex diseases
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DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124
Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673
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Global variation in copy number in the human genome
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Cited by
McCarthy, D. J., Chen, Y., & Smyth, G. K. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks042 · Cited by 5,195
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
De Jager, P. L., Srivastava, G., Lunnon, K., Burgess, J., Schalkwyk, L. C., Yu, L., Eaton, M. L., Keenan, B. T., Ernst, J., McCabe, C., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3786 · Cited by 956
“…data generated from the same brain DNA samples in four of the subjects (two non-impaired and two AD subjects): in these four subjects, we see a very strong correlation (mean r= 0.97) between the estimated levels of methylation generated by the two technologies, consistent with prior reports 15 .”
InfluentialSelf-citationBock, C., Kiskinis, E., Verstappen, G., Gu, H., Boulting, G., Smith, Z. D., Ziller, M., Croft, G. F., Amoroso, M. W., Oakley, D. H., et al. (2011) · Cell · doi:10.1016/j.cell.2010.12.032 · Cited by 1,009
Self-citationDistinct DNA methylomes of newborns and centenarians
Heyn, H., Li, N., Ferreira, H. J., Moran, S., Pisano, D. G., Gomez, A., Diez, J., Sanchez-Mut, J. V., Setien, F., Carmona, F. J., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120658109 · Cited by 802
Gu, H., Smith, Z. D., Bock, C., Boyle, P., Gnirke, A., & Meissner, A. (2011) · Nature Protocols · doi:10.1038/nprot.2010.190 · Cited by 745
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Metadata
- Authors
- Bock, C., Tomazou, E. M., Brinkman, A. B., Müller, F., Simmer, F., Gu, H., Jäger, N., Gnirke, A., Stunnenberg, H. G., & Meissner, A.
- Venue
- Nature Biotechnology
- Published
- 2010-09-19
- Volume
- 28
- Issue
- 10
- Pages
- 1106-1114
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2156165856
- Cited by
- 593
- References
- 66
- FWCI
- 23.87
- Type
- journal article
- Language
- en
- Open access
- green
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