Data Engineer Human Genetics
An estimated 300,000 people in the Netherlands have a hereditary predisposition to cancer. Currently, this information is collected and maintained separately at the eight Dutch clinical genetics centres. The Netherlands Genetic Tumour Risk Registry (NESTOR) aims to harmonize and unify these data silos to improve our ability to perform research and patient monitoring throughout the country.
We are looking for a data engineer to develop the necessary data infrastructure for NESTOR. Your mission is to move away from manual data entry and create a seamless, automated infrastructure. You will build the pipelines that enable secure transfer of hereditary cancer information from local EHRs at UMCs to a central national resource.
As research data engineer for the NESTOR project at Amsterdam UMC, you are the primary engineer implementing our local and national data integration strategy.
Your key responsibilities:
- Automated ETL-pipelines: design and implement robust ETL/ELT workflows to extract, transform and load data from clinical sources (e.g., Epic, Genesis) into the NESTOR registry;
- National interoperability: ensure all data transfers comply with national standards such as HL7 FHIR and the Health-RI architecture;
- Synchronization between UMCs: work together with technical teams at other Dutch UMCs to harmonize data models and ensure consistency in recording and sharing of hereditary cancer risks;
- Privacy & Security: implement pseudonymization and encryption protocols to protect sensitive genetic and clinical information, fully complying with GDPR and UMC-specific security standards;
- Registry development: collaborate with clinical geneticists and researchers to expand the capabilities of NESTOR and integrate new data types.
You are a technical specialist who wants your code to make a direct impact on public health. You enjoy the challenge of connecting diverse medical databases and creating a coherent whole.
You bring:
- a BSc, MSc or PhD in Computer Science, Bioinformatics or a comparable technical field;
- Expert knowledge of Python and advanced SQL. Experience with Containers and API development;
- Experience with working with clinical registries or EHR data (Epic/Genesis) is a strong advantage;
- Experience with medical data standards (OMOP, FHIR or SNOMED CT) is highly desirable;
- The ability to navigate the organizational complexity of the Dutch UMC landscape and to communicate effectively with both IT departments and medical specialists.
- You will be employed by Amsterdam UMC Research BV.
- A contract for 2 years.
- Classification in salary scale 10: € 3.598 to € 5.669 gross for full-time employment (depending on experience). In addition to a good basic salary, we offer 8.3% end-of-year bonus. Calculate your net salary here. As of 1 July 2026, the salary will be increased by 3.5% in accordance with the collective labor agreement (CAO UMC).
- Holiday hours: 194.4 per year for full time and a possibility to save additional hours.
- 100% reimbursement for public transport travel costs. If you travel by foot, bicycle, or car, a mileage allowance of €0.21 per km applies (up to a maximum of 40 km one way by car).
- Do you prefer walking or cycling? Take advantage of our good bike scheme.
- Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.
Watch this video with more information about joining Amsterdam UMC Research BV.
The position will be embedded in the Advanced Compute & Data Core (ACDC) team and the Laboratory Genome Analysis within the Department of Human Genetics. You will be part of the NESTOR project, a nationwide initiative to create a centralised registry for hereditary cancers.
The Advanced Compute & Data Core currently consists of a team of 7 HPC engineers, data engineers and data stewards. Our team is a result of close collaboration between the Omics and Bio-imaging core facilities at Amsterdam UMC and has the mission to provide an integrated compute & data platform.
The Laboratory Genome Analysis is part of the department of Human Genetics. Around 200 staff members work here, performing a variety of molecular tests to investigate hereditary genetic disease under ISO 15189 accreditation. Our lab routinely performs Whole Genome Sequencing (WGS) with state-of-the-art short read sequencing (Illumina) and long read sequencing (Oxford Nanopore) technologies.
Do you have questions about this position? Please contact dr. Daoud Sie, Head Bioinformatics, at d.sie@amsterdamumc.nl.
A reference check, screening and hiring assessment 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 will not be considered.
