In accordance to the latest edition of the WHO classification bluebook, tumors of the central nervous system (CNS) may be diagnosed with the use of genome-wide methylation profiling. Timely and accurate categorization of CNS tumor subtypes is pivotal for optimal patient management. The current diagnostic laboratory procedure and algorithm for classification has limitations that can be overcome with fast Nanopore-sequence technology and deep-learned neural-network driven classification called "Sturgeon”. In a proof-of-concept study we have shown that Sturgeon demonstrates exceptional accuracy and speed to predict the molecular CNS tumor (sub-)class, which awaits implementation in daily diagnostic practice.

The project is a collaborative effort between the Departments of Pathology and Neurosurgery of Amsterdam UMC on the one hand and the Center for Molecular Medicine at UMC Utrecht on the other.

Your role will be to get (Sturgeon based) Nanopore methylation profiling ready for implementation in daily diagnostic practice. Therefore you will perform retrospective as well as prospective experiments for several 100 adult-type diffuse glioma and meningioma tumor patients samples using nanopore sequencing and Sturgeon classification and compare these to current methylation profiling procedures. Thereby you will proactively lead this project within a multidisciplinary team of researchers, clinicians and AI experts from Amsterdam UMC and UMC Utrecht, combining wet-lab techniques and bioinformatic analyses. You will also take the lead in publishing your validation and implementation findings in peer-reviewed journals, while presentations at scientific conferences will be an integral part of your work.

• PhD in Molecular Biology or Bioinformatics;
  
  • Ability to optimize and streamline (laboratory) procedures
  • Proficiency in data management
• Wetlab experience with molecular biology techniques;
• Proficiency in bioinformatics tools and programming languages commonly used in genomics and cancer research (e.g., Python, R, C++);
• Experience with next-generation sequencing data analysis and genomic data interpretation;
• Excellent communication and collaboration skills.

• A 12-month contract with the possibility of extension for another 12 months.
• Salary scale 10: € 3.359 - € 5.292 with a 36 hour week (depending on qualifications and experience).
• Besides a good basic salary, you will also receive an 8.3% year-end bonus and 8% holiday allowance.
• Free and unlimited access to our online learning environment GoodHabitz.
• Pension accrual with BeFrank, a modern, understandable, and well-priced pension.
• Excellent accessibility by public transport and reimbursement of a large part of your transport costs. We also have a good bicycle scheme if you cycle,
• An active personnel association and the Young Amsterdam UMC association, both of which organize fun (sports) activities and events.

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

Amsterdam UMC

You will be based at the Cancer Center Amsterdam (CCA) at the Department of Pathology of Amsterdam UMC, location VUmc, with partial secondment to UMC Utrecht. The CCA‘s mission is to create groundbreaking new possibilities for patients with cancer. To achieve this, we integrate world-class research with healthcare and education to boldly push boundaries and discover new insights and opportunities. By making direct use of the knowledge obtained from our research, we strive to provide the best innovative and compassionate care for patients with cancer.