Postdoc Nanopore methylation sequencing for implementation in cancer diagnostics

Updated: 2 months ago
Deadline: 17 Apr 2024

3 Apr 2024
Job Information

Amsterdam UMC
Research Field

Researcher Profile

Recognised Researcher (R2)

Application Deadline

17 Apr 2024 - 21:59 (UTC)
Type of Contract

Job Status

Not Applicable
Hours Per Week

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme
Is the Job related to staff position within a Research Infrastructure?


Offer Description

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.

Specific Requirements
  • 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.

Additional Information
  • 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 .

Additional comments

The first round of interviews is scheduled for May 06, 2024. We ask you to take this into account in advance. The second round of interviews will follow in principle May 22, 2024.

If you have any questions about this position, please feel free to contact Bauke Ylstra, Hoogleraar via 020-4442495 or via [email protected] .

For more information about the application procedure, please contact Chey Edwards, Recruitment Advisor, via 06-21487245 or via [email protected] .

A reference check, screening and hiring test may be part of the procedure. Read here whether that applies to you. If you join us, we ask you for a VOG (Certificate of Good Conduct).

Internal candidates will be given priority over external candidates in case of equal suitability.

Acquisition in response to this vacancy is not appreciated.

Website for additional job details

Work Location(s)
Number of offers available
Amsterdam UMC
Postal Code
De Boelelaan 1117

Where to apply


Amsterdam Zuidoost

Meibergdreef 9
Postal Code

1105 AZ


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