dr. Andries De Koker (PhD)

I have been investigating novel library preparation methods for next generation sequencing (NGS), especially for the analysis of CpG-methylation of circulating cell-free DNA (cfDNA). cfDNA extracted from blood (“liquid biopsies”) has been proposed to be one of the most promising biomolecules for use in cancer screening, early tumor diagnosis and residual disease and therapy monitoring. However, cfDNA is highly fragmented and quantity is limited in the blood, making it also a difficult-to-handle biomolecule.
During my research I have tested many different library preparation methods and encountered many problems when working with low-input and low-quality DNA samples, hence I may have to offer some technical advice to researchers performing NGS-based experiments on a similar DNA input. Moreover, I also succeeded to develop a cost-effective methylome profiling method (termed ‘cf-RRBS’) that can be used on limited amounts (nanogram range) of highly degraded DNA (cfDNA, FFPE, …). cf-RRBS gives information about the methylation state of ±2.5 million CpGs at a cost of ±200 euro per sample.
Three collaborators at the Center of Medical Genetics of the UZ Ghent are currently testing this method to answer different clinical questions (e.g. in adult/pediatric oncology and pregnancy). Preliminary results show it is feasible to perform the cf-RRBS method in such clinical setting and the obtained methylation data is more than sufficient for tumor classification and biomarker discovery.
In the future, we hope that the cf-RRBS technology in its whole or in part can be used in clinic and this during all phases of personalized medicine (i.e. screening, early diagnosis and prognosis, residual disease and therapy monitoring). Faster and more informative monitoring of the individual patients will eventually result in precise and more effective treatment.
 

• Lab address: Technologiepark 75 9052 Zwijnaarde
• VIB-UGent Center for Medical Biotechnology 
• Available for other researchers: Femto Pulse Analyzer (AATI-Agilent)
• Andries De Koker is interested to receive invitations for presentations or talks