Pharmaco Diagnostics - Biomarker Discovery

Genome-wide epigenetic profiling

Epigenetic treatment followed by expression arrays (pharmacological unmasking) identifies transcripts under control of methylation. This approach, which results in genes that are functionally responding to the treatment by being re-expressed, has provided numerous novel cancer-specific methylation events over the past decade.

This approach is being complemented by MBD2_Seq, which is more open-ended, as no prior probes need to be spotted on an array, and results in a true genome-wide epigenetic profile. The workflow has been further perfected and downsized in order to handle small fresh clinical samples.

Candidate Genes Approach

MSP, methylation specific PCR, in medium to high throughput allows the examination of hundreds of samples for hundreds of genes. Precompiled arrays, called prediction arrays, containing all DNA damage and response genes have been tested on many different samples types ranging from cell lines, xenografts till primary samples of different origin and matched normals.

In addition to MSP we typically run deep sequencing profiles on primary material to lock the position of the primers by 454 bisulphite sequencing.