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PMID: 20852634 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Quantitative comparison of genome-wide DNA methylation mapping technologies.

Nature biotechnology ·Vol. 28 ·No. 10 ·2010-10-00 ·Pages 1106-14

Bock C, Tomazou EM, Brinkman AB, Müller F, Simmer F, Gu H, Jäger N, Gnirke A, Stunnenberg HG, Meissner A

Abstract

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.

MeSH Terms
Aged, 80 and over Cell Line DNA Methylation/genetics Genome, Human/genetics Humans Male Repetitive Sequences, Nucleic Acid/genetics Reproducibility of Results Sequence Analysis, DNA/methods
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Bock Christoph
Broad Institute, Cambridge, Massachusetts, USA. [email protected]
Tomazou Eleni M
Brinkman Arie B
Müller Fabian
Simmer Femke
Gu Hongcang
Jäger Natalie
Gnirke Andreas
Stunnenberg Hendrik G
Meissner Alexander
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.1681
Email
[email protected]
Published
2010-10-00
Epub
2010-00-19
Pages
1106-14
Language
English
Region
United States
NLM ID
9604648
PMCID
PMC3066564
Subset
IM
Grants
NIEHS NIH HHS · U01 ES017155 · United States
NIEHS NIH HHS · U01 ES017155-04 · United States
NIEHS NIH HHS · U01ES017155 · United States
Corrections
CommentIn
PMID: 20944589
External Links
PubMed source DOI: 10.1038/nbt.1681 PMC Full Text View journal details
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