Skip Navigation


Nucleic Acids Research Advance Access originally published online on September 13, 2007
Nucleic Acids Research 2007 35(18):e119; doi:10.1093/nar/gkm662
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4009K) Freely available
Right arrow Screen PDF (939K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
35/18/e119    most recent
gkm662v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Coolen, M. W.
Right arrow Articles by Clark, S. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Coolen, M. W.
Right arrow Articles by Clark, S. J.
Related Collections
Right arrow Nucleic acid modification
Right arrow Genomics
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2007, Vol. 35, No. 18 e119
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements

Marcel W. Coolen, Aaron L. Statham, Margaret Gardiner-Garden and Susan J. Clark*

Cancer Program, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney 2010, New South Wales, Australia

*To whom correspondence should be addressed. Tel: +61 2 92958315; Fax: +61 2 92958316; Email: s.clark{at}garvan.org.au

Received June 22, 2007. Revised August 1, 2007. Accepted August 11, 2007.

CpG methylation is a key component of the epigenome architecture that is associated with changes in gene expression without a change to the DNA sequence. Since the first reports on deregulation of DNA methylation, in diseases such as cancer, and the initiation of the Human Epigenome Project, an increasing need has arisen for a detailed, high-throughput and quantitative method of analysis to discover and validate normal and aberrant DNA methylation profiles in large sample cohorts. Here we present an improved protocol using base-specific fragmentation and MALDI-TOF mass spectrometry that enables a sensitive and high-throughput method of DNA methylation analysis, quantitative to 5% methylation for each informative CpG residue. We have determined the accuracy, variability and sensitivity of the protocol, implemented critical improvements in experimental design and interpretation of the data and developed a new formula to accurately measure CpG methylation. Key innovations now permit determination of differential and allele-specific methylation, such as in cancer and imprinting. The new protocol is ideally suitable for detailed DNA methylation analysis of multiple genomic regions and large sample cohorts that is critical for comprehensive profiling of normal and diseased human epigenomes.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Cancer Res.Home page
M. Camoriano, S. R. Morey Kinney, M. T. Moser, B. A. Foster, J. L. Mohler, D. L. Trump, A. R. Karpf, and D. J. Smiraglia
Phenotype-Specific CpG Island Methylation Events in a Murine Model of Prostate Cancer
Cancer Res., June 1, 2008; 68(11): 4173 - 4182.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.