Project description: In the Netherlands, 7600 women are diagnosed yearly with an ovarian tumor. Only about 5% of these tumors are malignant. It is very important to accurately identify these malignant tumors prior to surgery to ensure proper treatment. Unfortunately, this can be very challenging. In this project, we aim to find specific molecular biomarkers in liquid biopsies that can efficiently discriminate between benign and malignant ovarian tumors with a sensitivity of at least 90% and a specificity of at least 80%. We will determine genetic abnormalities (mutations, copy number aberrations and chromosomal abnormalities) in circulating tumor DNA and RNA profiles of tumor educated platelets (TEPs). We will develop novel computational approaches to analyze these unique datasets separately and jointly, to arrive at accurate predictors to identify malignant tumors from liquid biopsies.

Interdisciplinary collaboration: The groups of Lodewyk Wessels and Marcel Reinders and (NKI and TUDelft) will develop advanced machine learning approaches to construct (integrative) predictors from the different data streams. The supervisory team will be strengthened by the pathology expertise of Hugo Horlings (NKI) and collaborations with Victor Velculescu at Johns Hopkins (circulating copy number profiles from circulating DNA) and Tom Wurdinger at the VUMC (TEPs). The project is embedded within broad oncological collaborations within the VUMC, LUMC, Catharina Ziekenhuis in Eindhoven and the NKI. The successful candidate will be employed at the NKI and will spend at least two days per week at the TUDelft. Regular meetings between project partners will be held to generate sufficient cohesion and momentum.

We are seeking a highly motivated PhD candidate with:

• A degree in bioinformatics, computer science or a related discipline
• Proficiency in bioinformatics programming languages (e.g. R, Python)
• Good cross-disciplinary collaborative and communication skills
• Experience in statistics, machine learning and/or pattern recognition is a plus
• Experience in analysing high-throughput molecular data is a plus
• Experience in cancer biology and clinical applications is a plus.

Fixed-term contract: 4 jaar.

The appointment will initially be for 4 years and the gross salary per month will range from € 2.798,- to €3.446,- depending on your experience. The terms of employment will be in accordance with the CAO Ziekenhuizen (Collective Labour Agreement for Hospitals).

Antoni van Leeuwenhoek

Het Antoni van Leeuwenhoek is hét in kanker gespecialiseerde ziekenhuis en onderzoeksinstituut. Sinds de oprichting in 1913 combineert het Antoni van Leeuwenhoek de zorg voor kankerpatiënten met grensverleggend onderzoek. Wij gaan voor de beste zorg voor elke patiënt. Want kanker, dat kan iedereen overkomen.