You will participate and be a key player in a multicenter prospective diagnostic accuracy study that aims to develop, validate and implement novel Non-Invasive Prenatal Diagnosis (NIPD) for monogenic diseases in the clinic. NIPD promises a prenatal diagnostic blood test that can be offered to pregnant couples opting for prenatal diagnosis because they know they are carrier of a severe monogenic disease. Such couples now rely for diagnosis on invasive surgery procedures: NIPD will be the much-desired non-invasive and less burdensome alternative. NIPD involves the analysis of the fetal fraction of cell-free DNA present in plasma of the pregnant mother: based on long-read sequencing-deduced haplotypes of the parents, we will analyze the cfDNA composition during pregnancy, to accurately determine which allele each parent transmitted to the offspring. PhD student will be co-responsible for the development of sophisticated analytical tools for long-read sequencing-based haplotyping and for cfDNA analysis, for the development of a robust statistical framework for NIPD, for the analysis  and diagnosis of pregnancies included in this study and for NIPD implementation in the clinic. PhD student will work under shared supervision by a senior bioinformatician and by Prof. Wouter de Laat, and in close collaboration with our clinical bioinformatics team, the Genomics Diagnostics section and with other relevant UMCU research groups such as the AI research group headed by Prof. Dr. Jeroen de Ridder.

You will join a growing team of enthusiastic translational researchers at the Genetics Research Section. This section has five principle investigators and is headed by Prof. Dr. Wouter de Laat. We are embedded within the Department of Genetics at the UMC Utrecht. Within our Department we collaborate with Clinical Geneticists constantly counseling new patients, Genome Diagnostics, who sequence thousands of patients per year based on the latest, most state-of-the-art, sequencing platforms (both short and long read), the Metabolic Diagnostics, who use untargeted metabolomics for their patients, and Clinical Bioinformatics, headed by Dr. Hanneke van Deutekom, for the most responsible and smooth processing of all diagnostics datasets using several bioinformatic workflows. It is our shared mission to improve clinical genetic care through implementation of technical developments and advancing genetic analysis.

We are looking for a PhD student with the following profile:

• MSc in bioinformatics.
• Advanced knowledge of Python, R and Bash, knowledge of Nextflow is a plus. 
• Experience in the fields of statistics, NGS data analysis, and preferably, genetics. 
• Experience with long read sequencing an/or cfDNA analysis is a plus. 
• Experience with human genetics and monogenic disorders is a plus.
• Keen interest in translational research and societal impact.
• Personality: curiosity driven, translational researcher, team player, broad interest, independent. 
• Proficient in English.

• A salary between €3017 and €3824 gross per month (salary scale OIO), based on full-time employment (36 hours).
• Salary increase of 3% from July 2025, according to the collective labor agreement (cao).
• Year-end bonus of 8.3% and holiday allowance of 8%.
• Pension insurance with ABP. We take care of approximately 70% of the monthly contribution.
• 100% public transport reimbursement. Are you coming on foot, by bike or by car? You will then receive a reimbursement of € 0.18 per km (by car up to a max. of 40 km one way).
• Possibilities to develop yourself personally and professionally.
• The option to select additional employment benefits in exchange for gross salary, such as purchasing a bicycle and memberships.