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Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis

Item Type:Article
Title:Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis
Creators Name:Uhlmann, K. and Brinckmann, A. and Toliat, M.R. and Ritter, H. and Nuernberg, P.
Abstract:Tumorigenesis is characterized by alterations of methylation profiles including loss and gain of 5-methylcytosine. Recently, we identified a single CpG, which seemed to be consistently hypomethylated in pilocytic astrocytomas but not in other gliomas. To evaluate its applicability as a biomarker, we examined its methylation status in a large panel of gliomas (n = 97). Methylation-dependent DNA sequence variation may be considered a kind of single nucleotide polymorphism (methylSNP). MethylSNPs can be easily converted into common SNPs of the C/T type by sodium bisulfite treatment of the DNA and afterwards subjected to conventional SNP typing. We adapted SnaPshot™ and Pyrosequencing™ to determine the methylation of our test CpG in a quantitative manner. The adapted methods, called SNaPmeth and PyroMeth, respectively, gave nearly identical results, however data obtained with PyroMeth showed less scattering. Furthermore, the integrated software for allele frequency determination from Pyrosequencing could be used directly for data analysis while SnaPmeth data had to be exported and processed manually. Although data did not confirm our previous result of a preferential hypomethylation of the tested CpG in pilocytic astrocytomas, we consider quantitative methylSNP analysis by SNaPmeth or PyroMeth a favorable alternative to existing high-throughput methylation assays. It combines single CpG analysis with accurate quantitation and is amenable to high throughput.
Keywords:Biomarker, DNA Methylation, Glioma, Hypomethylation, Methyl-Single Nucleotide Polymorphism
Source:Electrophoresis
ISSN:0173-0835
Publisher:Wiley (Germany)
Volume:23
Number:24
Page Range:4072-4079
Date:December 2002
Official Publication:https://doi.org/10.1002/elps.200290023
PubMed:View item in PubMed

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