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This Article Full Text Full Text (PDF) Data Supplement All Versions of this Article: clinchem.2007.072629v1 53/1/17    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Web of Science (10) Citing Articles via Google Scholar Google Scholar Articles by Brakensiek, K. Articles by Lehmann, U. Search for Related Content PubMed PubMed Citation Articles by Brakensiek, K. Articles by Lehmann, U. Related Collections Molecular Diagnostics and Genetics

Quantitative High-Resolution CpG Island Mapping with Pyrosequencing^TM Reveals Disease-Specific Methylation Patterns of the CDKN2B Gene in Myelodysplastic Syndrome and Myeloid Leukemia

¹ Institute of Pathology, Medizinische Hochschule Hannover, Hannover, Germany.
² Department of Disease and Stress Biology, John Innes Centre, Norwich, England.

^aAddress correspondence to this author at: Institute of Pathology, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, D-30625 Hannover, Germany. Fax 49-511-532-5799; e-mail Lehmann.Ulrich{at}MH-Hannover.de.

Background: Gene silencing through aberrant CpG island methylation is the most extensively analyzed epigenetic event in human tumorigenesis and has huge diagnostic and prognostic potential. Methylation patterns are often very heterogeneous, however, presenting a serious challenge for the development of methylation assays for diagnostic purposes.

Methods: We used Pyrosequencing^TM technology to determine the methylation status of 68 CpG sites in the CpG island of the CDKN2B gene [cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)], frequently hypermethylated in myeloid malignancies, in a series of bone marrow samples from patients with myelodysplasia and myeloid leukemia (n = 82) and from 32 controls. A total of 7762 individual methylation sites were quantitatively evaluated. Precision and reproducibility of the quantification was evaluated with several overlapping primers.

Results: The use of optimized sequencing primers and the new Pyro Q-CpG^TM software enabled precise and reproducible quantification with a single sequencing primer of up to 15 CpG sites distributed over 100 bp. Extensive statistical analyses of the whole CpG island revealed for the first time disease-specific methylation patterns of the CDKN2B gene in myeloid malignancies and small regions of differential methylation with high discriminatory power that enabled differentiation of even low-grade myelodysplastic syndrome samples from the controls, a result that was confirmed in an independent group of 9 control and 36 patient samples.

Conclusion: The precise quantitative methylation mapping of whole CpG islands is now possible with Pyrosequencing software in combination with optimized sequencing primers. This method reveals disease-specific methylation patterns and enables the development of specific diagnostic assays.

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