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

被引:119
作者
Uhlmann, K
Brinckmann, A
Toliat, MR
Ritter, H
Nürnberg, P
机构
[1] Max Delbruck Ctr Mol Med, Gene Mapping Ctr, D-13902 Berlin, Germany
[2] Humboldt Univ, Inst Med Genet, Charite Univ Hosp, Berlin, Germany
关键词
biomarker; DNA methylation; glioma; hypomethylation; methyl-single nucleotide polymorphism;
D O I
10.1002/elps.200290023
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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(TM) and Pyrosequencing(TM) 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.
引用
收藏
页码:4072 / 4079
页数:8
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