Edwin Cuppen Group

Edwin Cuppen

Oncode Investigator at Hubrecht Institute

My Research

Edwin Cuppen (1970) obtained his masters in molecular sciences at the Agricultural University Wageningen in 1994 (cum laude) and his PhD degree in 1999 at the Radboud University in Nijmegen in the group of Prof. Be Wieringa. During his education, he spent half a year in het Jaenish lab at the Whitehead Institute in Boston. From 1999 to 2002 he performed postdoctoral research at the Netherlands Cancer Institute in Amsterdam and the Hubrecht Institute in Utrecht, The Netherlands, in the group of Prof. Ronald Plasterk. In 2002 he became staff scientist at the Hubrecht Institute and in 2007 he was appointed professor of Genome Biology at the Biology department of the Utrecht University. In 2009 he was appointed professor of Human Genetics and head of the research section of the Medical Genetics department of the University Medical Center Utrecht, while continuing his work at the Hubrecht Institute with a split appointment. In 2015, he left the Hubrecht Insitute to transfer his research group completely to the UMC Utrecht and to become the director of the Center for Molecular Medicine (23 research groups, ~250 scientists). In 2017, he stepped down from this position and became director of the Hartwig Medical Foundation in Amsterdam, while remaining associated with the UMC Utrecht for his fundamental research activities.

His area of expertise is in genomics and genetics and his scientific interests are in functional and personal genomics. In 2005, Edwin Cuppen was awarded a European Young Investigators Award for his work on naturally occurring and induced genetic variation in the laboratory rat. He was one of the first to generate gene knockout models in the rat and showed the widespread effect of copy number variation on gene expression levels. In 2013, he was awarded a prestigious NWO Vici grant for dissecting the molecular mechanisms behind structural genomic variation and studying the functional consequences using integrated systematic -omics approaches.

In his current work he combines experimental methods, including next-generation sequencing technology, patient material and model systems like organoids, with bioinformatic approaches to understand the effects of genetic variation under normal and disease conditions, with a specific focus on cancer and congenital disease. His research group has a long track record in high-throughput DNA analysis and was among the first to pioneer next-generation sequencing (NGS) technology. His group developed and improved various NGS-based techniques and is now routinely applying NGS-based techniques in a wide range of systems from human patients to animal models and adult stem cell culturing systems (normal and tumor derived organoids). His group has specialized in studing genomic structural variation and they are using NGS-based techniques like (small) RNA sequencing, ChIP-Seq, and 4C-seq to detect molecular consequences and dissect underlying biological mechanisms. Furthermore, within the Medical Center settings, he is involved in implementing NGS approaches for diagnostic purposes in clinical genetics and personalized cancer treatment (cofounder of Center for Personalized Cancer Treatment).

Edwin Cuppen is also scientific founder and director of the Hartwig Medical Foundation (2015) in Amsterdam, which operates an Illumina Xten setup for large scale whole genome sequencing and in which national clinical and research parties collaborate for improving personalized cancer patient care. HMF has generated one of the largest cancer whole genome sequencing databases worldwide.

Edwin Cuppen is also an inventor on various patents and cofounder of the biotech startup company InteRNA Technologies that focuses on miRNA-based diagnostics and therapeutics. He has been advisor for several biotech startups in the area of genomics technology and bioinformatics.


  • 2013: NWO Vici
  • 2005: European Young Investigators Award (EURYI) (European Science Foundation)

Key publications

  1. Blokzijl, F., De Ligt, J., Jager, M., Sasselli, V., Roerink, S., Sasaki, N., ... & Nijman, I. J. (2016). Tissue-specific mutation accumulation in human adult stem cells during life. Nature, 538(7624), 260.
  2. Drost, J., Van Boxtel, R., Blokzijl, F., Mizutani, T., Sasaki, N., Sasselli, V., ... & Nik-Zainal, S. (2017). Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Science, 358(6360), 234-238.
  3. Jager, M., Blokzijl, F., Sasselli, V., Boymans, S., Janssen, R., Besselink, N., ... & Cuppen, E. (2018). Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures. Nature protocols, 13(1), 59.
  4. Sachs, N., de Ligt, J., Kopper, O., Gogola, E., Bounova, G., Weeber, F., ... & Korving, J. (2017). A living biobank of breast cancer organoids captures disease heterogeneity. Cell.
  5. Van Heesch, S., Simonis, M., van Roosmalen, M. J., Pillalamarri, V., Brand, H., Kuijk, E. W., ... & Hao, W. (2014). Genomic and functional overlap between somatic and germline chromosomal rearrangements. Cell reports, 9(6), 2001-2010.
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Edwin Cuppen Oncode Investigator

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