Identification of pan-cancer and tumor-specific methylation based biomarkers and development of bioinformatics infrastructure for a novel multiplex methylation assay
Description: With an estimated 8.8 million deaths yearly, the cancer burden weighs heavily on populations globally. Early detection of cancer is one of the key aspects that results in improved patient prognosis. In this respect, the analysis of circulating tumor DNA in plasma is potentially a major enhancement over currently used imaging, immunochemincal or histopathological methods. Highly sensitive and specific biomarkers for the most common types of cancer are currently still lacking however. In light of recent publications, DNA methylation holds great promise as a tumour marker, but it is yet to be fully explored in the context of liquid biopsies. Our preliminary data shows that CpG methylation can be used to effectively detect cancer and determine different tumors. Our research group is developing a new, robust, and cost-effective diagnostic assay using methylation markers, termed MeD-smMIPs-seq. This assay will combine methylated DNA sequencing with single molecule molecular inversion probes to target highly informative CpGs and achieve high diagnostic sensitivity while reducing assay costs. The aim of this project is first to identify the most informative differentially methylated regions genome-wide, that can be used as cancer biomarkers in this assay. Secondly, we aim to develop the bioinformatics framework required for new experimental design and downstream data analysis. Finally, we will validate the assay and the computational pipeline in the context of liquid biopsies.
Funder: Fonds Wetenschappelijk Onderzoek
Funding type: fellowship
Funder scheme: FWO fellowships
Start date: 2019-11-01
End date: 2021-10-31
Investigator: Joe Ibrahim
Institution: FWO
Funded outputs count: 7
Funder award ID: 11B5220N
OpenAlex ID: G252277702