PhD on complex trait analysis using low-pass cell-free DNA sequence data

Katholieke Universiteit Leuven


August 20, 2021


PhD on complex trait analysis using low-pass cell-free DNA sequence data

(ref. BAP-2021-591)

Last modification : Friday, July 9, 2021

The Cleynen (Complex Genetics) and Kivisild (Evolutionary and Population Genetics) labs are dynamic teams of driven, enthusiastic and inclusive scientists. We aim to develop, test and use bioinformatics approaches to utilize biobank-scale data of whole genome low-pass cell-free DNA sequences for the study of complex traits using genotype imputation and polygenic risk score approaches.

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In this position, you will play a key role in the FWO funded MICADO (Multiomic Integration of cell-free DNA profiles to Advance Disease Outcome) research consortium that strives to maximize the diagnostic and prognostic potential of cell-free DNA (cfDNA) analyses by combining multiple omics layers, with the aim to deliver superior methods for patient stratification and thus improve patient care.

Project background: Genomic medicine moves health care from being reactive to disease to being predictive to disease onset or from cure to prevention. Next-generation sequencing technologies have leveraged novel concepts to diagnose, treat and monitor diseases. Analysis of free- floatingcfDNA from blood or other body fluids - called “liquid biopsy” - represents an emerging tool that enables non-invasive monitoring of tissue dynamics in multiple human physiological and pathological conditions, including pregnancy, cancer and other conditions. The MICADO partners are developing innovative approaches for (epi)genome-wide cfDNA analysis that can lead to novel applications to monitor health and disease.

In this project we will increase the cfDNA knowledge base, develop novel analysis tools for mining and integration of cfDNA genomic and epigenome data that could enable development of new liquid biopsy-derived biomarkers. Apart from disease-specific(diagnostic) biomarkers, we will also leverage the full potential of (epi)genomic data for personalized polygenic risk scores assessments to enable patient stratification and guided patient/disease management. The integrationof multi-omics data will provide novel and unique approaches for patient stratification, population screening as well as disease detection. Our technology will allow for earlier intervention, improve patient outcomes, increase overall population health and reduce health care costs.


You ideally have:

  • a keen interest and motivation to work on ambitious projects in a dynamic, driven team;
  • the ability to meet timelines and work accurately;
  • a passion for analyzing high-throughput sequencing data;
  • a Master's degree in bioinformatics, population genetics, biomedical sciences, or equivalent qualifications;
  • experience in complex trait or biobank-scale data analyses, statistics, or programming (desirable, not a prerequisite).
  • You will:

  • work with and responsibly manage large genomic data sets on the VSC computing environment;
  • develop pipelines for population genetics, statistical, and complex trait analyses on the data;
  • communicate results in a professional manner in spoken and written English through papers, presentations and discussions with consortium members;
  • coordinate with other team members on cfDNA analyses.
  • You must hold a Master's degree when commencing the post.


    Working with us: We have onsite access to state-of-the-art facilities, including high-throughput sequencing, bioinformatics, imaging, high-capacity computing, single cell analysis platforms, flow cytometry and others. We are committed to inclusivity and diversity in the workplace, and value a positive, empowering and actively engaging attitude in every team member.

    Located in Leuven, a small but vibrant and international town by the river Dijle where centuries of history meet cutting-edge science, we are only a stone's throw away from the cosmopolitan city of Brussels, the heart of Europe. We are part of the University of Leuven, one of the oldest and most prestigious universities of Europe. Founded in 1425, it is Belgium's largest university, currently featuring among the best universities in the world according to the Times Higher Education and recently ranked as Europe's most innovative for the third year in a row.

    We offer a 4-year position on a competitive salary, pending positive evaluation by our doctoral school after 1 year.

    The earliest start date of the position is October 1st, 2021, but we are very happy to cater this for the ideal candidate.


    For more information please contact Prof. dr. Isabelle Cleynen, mail: or Prof. dr. Toomas Kivisild, mail:

    KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at

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