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Nucleic Acids Research, 2003, Vol. 31, No. 9 e50
© 2003 Oxford University Press

Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry

Jörg Tost, Philipp Schatz1, Matthias Schuster1, Kurt Berlin1 and Ivo Glynne Gut

Centre National de Génotypage, Bâtiment G2, 2 Rue Gaston Crémieux, CP 5721, 91057 Evry Cedex, France and 1 Epigenomics AG, Kastanienallee 24, 10435 Berlin, Germany

*To whom correspondence should be addressed. Tel: +33 160 87 2500; Fax: +33 160 87 83 83; Email: ivogut{at}cng.fr

As the DNA sequence of the human genome is now nearly finished, the main task of genome research is to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the development of cancer. Even minor changes in the degree of methylation can have severe consequences. An accurate quantification of the methylation status at any given position of the genome is a powerful diagnostic indicator. Here we present the first assay for the analysis and precise quantification of methylation on CpG positions in simplex and multiplex reactions based on matrix-assisted laser desorption/ ionisation mass spectrometry detection. Calibration curves for CpGs in two genes were established and an algorithm was developed to account for systematic fluctuations. Regression analysis gave R2 >= 0.99 and standard deviation around 2% for the different positions. The limit of detection was ~5% for the minor isomer. Calibrations showed no significant differences when carried out as simplex or multiplex analyses. All variable parameters were thoroughly investigated, several paraffin-embedded tissue biopsies were analysed and results were verified by established methods like analysis of cloned material. Mass spectrometric results were also compared to chip hybridisation.


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