The basis for the above mentioned NGFN platform was laid in an earlier collaborative projects with Frank Lyko (Division of Epigenetics, DKFZ) as well as the company Epigenomics in Berlin, funded by the Deutsche Forschungsgemeinschaft.
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In a pilot study, we studied the CpG island in the promoter region of the tumour suppressor gene p16. In total, 876 oligonucleotide probes of 21 nucleotides in length were used to inspect the methylation status of 53 CpG dinucleotides, producing correct signals in colorectal cancer cell lines as well as control samples with a defined methylation status. The information was validated by established alternative methods. The overall methylation pattern was consistent for each cell line, while different between them. At the level of individual cytosines, however, significant variations between individual cells of the same type were found, but also consistencies across the panel of cancer cell lines.
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In addition, we also developed alternative modes and techniques for an on-chip detection- For example, primer extension reactions were developed, which reduced significantly the number of oligonucleotides needed for an analysis. and concomitantly increased the accuracy of base calling, since the process combines binding to a complementary oligonucleotide with the specificity of the polymerase.

For this purpose, we used and modified in a collaboration the APEX system established in the group of Andres Metspaly (Tartu University, Estonia). In this process, the chip-bound primers hybridise to the genomic sequence directly adjacent to the base of interest. Upon an incubation with labelled dideoxynucleotides, the fitting nucleotide is incorporated by the polymerase and can be detected by means of the specific fluorophore.