PhD student | Liquid Biopsy

Diffuse Large B cell Lymphoma (DLBCL) is the most common aggressive (fast-growing) Non-Hodgkin-lymphoma with heterogeneous clinical outcome and molecular characteristics. Despite being an aggressive lymphoma, DLBCL is considered potentially curable. Unfortunately, a large proportion of patients do not benefit from standard first-line therapy but promising individualized therapies such as CAR-T cell therapy are under development. To better asses which patients are eligible for new innovative therapies, accurate response prediction models need to be developed. We are building a dynamic model based on data from serial liquid biopsies, tissue and imaging. Preliminary evidence suggest that machine learning-powered diagnostic tools based on sequenicng of cell-free nucleaic acids shed by tumors into circulation may forecast which individual patient is likley to respond to therapy.

You will work with state-of-the-art sequencing technologies to profile blood samples in search of molecular signatures that predict outcome. These blood samples are collected in nationwide and international trials for DLBCL patients being treated in first-line. Specifically you will look for advancements in cell-free DNA and cell-free RNA extraction and detection including the use of nanometer-sized extracellualr vesicles (EV) as biosource. EVs are functional cell-cell communicators that drive tumor-progression and immunescape. State of the art cfDNA analysis includes fragmentomics and methylation while EV-RNA analysis will be performed with deconvolution to assess EV tissue origin.

You will work closley with experienced bioinformaticians and two other PhDs appointed to this project that ultimately should lead to a dynamic integrated risk-model based on blood, tissue and imaging data. By extension, this project will help built a framework to determine the efficacy of (novel) drugs in individual lymphoma patients in a clinical interventional trial.

We are seeking an aspiring researcher (MSc) in the fields of molecular biology/genomics with:

• Proven affinity for cancer and/or immunology research;
• Experience with genomic analysis from high-throughput sequencing data and affinity with statistics/machine learning will be a plus;
• The ability to work independently, and thrive in a multi-disciplinary academic environment and communicate fluently in English, verbally and in writing.

• A flying start to your career in scientific research.
• Plenty of room for personal development with a wide range of training & development of academic skills
• Working on large-scale and own research, with motivated colleagues
• The funds for this position are available for 4 years. We offer an initial contract for 12 months that can be extended (after evaluation) for another 36 months.
• Salary scale OIO: € 3.017 tot € 3.824 bruto (based on a fulltime workweek), depending on qualifications and experience.
• Additional benefits including an 8.3% end-of-year bonus and 8% holiday pay. Calculate your net salary here.
• Your pension is accrued at BeFrank. A modern, understandeble en fair pension
• Excellent accessibility with public transportation and reimbursement of a large portion of your travel expenses. Additionally, we have plenty of parking spaces at the AMC location and a good bicycle scheme.

For more information about our employment conditions, please visit our website.

For Dutch citizens it is mandatory to provide a VOG (a declaration of good behaviour).

You will be housed in the Exosomes Research Group, an internationally-oriented laboratory embedded in the department of Pathology at Amsterdam UMC. You will closely collaborate with the department of hematology and radiology, pioneering combinatiorial approaches for non-invasive (molecular) diagnostics. We work with large collections of patient material from different clinical studies and serially bio-banked samples stored at the liquid biopsy center of the Cancer Center Amsterdam (CCA). You will be part of the joint graduate school of Amsterdam UMC Cancer Center Amsterdam and Netherlands Cancer Institute, VU and UvA (OOA) dedicated to the training of more than 1000 PhD students working in the field of Oncology. Finally, you will collaborate with the CRUK Manchester Institute Cancer Biomarker Centre, with Dr Mouliere, an international expert in next-generation cfDNA analysis.