Collaboration between Tytgat and Kemmeren groups.
As a bioinformatician, I’m working in close collaboration with my colleagues to study the aberrations found in cell-free DNA (cfDNA), and compare them to those found in tumor DNA. We are adapting existing WES pipelines that detect short variants from tumor DNA to detect short variants from circulating tumor DNA in cfDNA. Having matching pipelines for liquid and tumor biopsies will allow us to cross check different aberrations in the tumor DNA and cfDNA per patient, with the goal of finding cfDNA biomarkers for clinical purposes.
We are also investigating the potential of cfDNA as a biomarker for renal cancer. Through cell-free reduced representation bisulfites sequencing (cfRRBS), we analyze the tumor’s methylation pattern to differentiate between tumor types. To do this, we are implementing an existing cfRRBS pipeline in our group that detects methylation patterns and uses them to predict the tumor entity present in a sample.
To summarize, we use liquid biopsies to study tumor heterogeneity, support and improve initial diagnosis, and evaluate the response to therapy and early detection of relapse.