Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection | Zendy

Philipp Schatz | Zendy; Jürgen Distler | Zendy; Kurt Berlin | Zendy; Matthias Schuster | Zendy

Open Access

Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection

Author(s) -

Philipp Schatz,

Jürgen Distler,

Kurt Berlin,

Matthias Schuster

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl218

Subject(s) - biology , methylation , dna methylation , dna microarray , microbiology and biotechnology , cpg site , carcinogenesis , peptide nucleic acid , microarray , gene , nucleic acid , computational biology , cancer research , genetics , gene expression

The methylation of CpG dinucleotides has become a topic of great interest in cancer research, and the methylation of promoter regions of several tumor suppressor genes has been identified as a marker of tumorigenesis. Evaluation of DNA methylation markers in tumor tissue requires hundreds of samples, which must be analyzed quantitatively due to the heterogeneous composition of biological material. Therefore novel, fast and inexpensive methods for high throughput analysis are needed. Here we introduce a new assay based on peptide nucleic acid (PNA)-library hybridization and subsequent MALDI-TOF analysis. This method is multiplexable, allows the use of standard 384 well automated pipetting, and is more specific and flexible than established methods, such as microarrays and MS-SNuPE. The approach was used to evaluate three candidate colon cancer methylation markers previously identified in a microarray study. The methylation of the genes Ade-nomatous polyposis coli (APC), glycogen synthase kinase-beta-3 (GSK3beta) and eyes absent 4 (EYA4) was analyzed in 12 colon cancer and 12 normal tissues. APC and EYA4 were confirmed as being differentially methylated in colon cancer patients whereas GSK3beta did not show differential methylation.

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