LUMC Research themes

The Medical Genomics theme supports, connects, and inspires LUMC researchers who study human health and disease through the lens of the genome.

Vision and mission

Medical Genomics aspires to understand the genomic bases of disease and spur on personalised therapies by applying and integrating genomic and other forms of data. This includes functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis, pharmacogenomics, and high-resolution phenotyping. The theme covers the full innovation pipeline from fundamental to translational, as well as from translational to clinical research. By fostering a stimulating Medical Genomics community, the theme will further advance the LUMC’s national and international position within the field.

“In the long history of humankind (and animal kind, too) those who learned to collaborate and improvise most effectively have prevailed”- Attributed to Charles Darwin

About us

Bas Heijmans, Scientific Coordinator and Professor of Population Epigenomics

Bas Heijmans is a Scientific Coordinator and a Professor of Population Epigenomics in the Department of Biomedical Data Sciences. “It is my drive to understand how the regulation of our genome is tuned by both environmental signals and genetic make-up, and the impact this process has on our health throughout life. To this end, my group integrates interconnected omics layers (for example, genome, epigenome, transcriptome) in population studies, develops methods and software tools, and applies causal inference methods and cell models to uncover causal mechanisms.”

Sylvie Noordermeer, Assistant Professor in the Department of Human Genetics and Oncode group leader

“I have always been intrigued why a healthy cell all of a sudden turns malignant. My group studies the (genetic) differences between healthy and cancerous cells and how genetic mistakes driving cancer can go unnoticed to the DNA damage repair mechanisms that should be in place to prevent tumorigenesis. For this, we combine a wide variety of approaches, including biochemistry, molecular biology, genomics and clinical data mining.”

 

Gijs Santen, Clinical Geneticist in the Department of Clinical Genetics

“My inspiration flows from the patients I see and the questions they have: it is a joy to continuously work on improving our ability to diagnose rare diseases, increasing the information we can give patients, and starting the search for treatment options. My group focuses on Coffin-Siris syndrome as a model for rare disorders, and on broadening the application and increasing the impact of extensive genetic testing, for example, during pregnancy.”

 

Contact

Please email us with all your questions and if you wish to join our community as an LUMC researcher. Email: MedicalGenomics@lumc.nl

Research collaborations and alliances

• Leiden Genome Technology Center (LGTC)
• Sequence Analysis Support Core (SASC) 
• GenomeScan
• Data Analytics
• BBMRI-NL
• Leiden Center of Data Science
• Dutch Center for RNA Therapeutics (DCRT)

Opportunities

Read more

• Our vacancies
• Internships for Biomedical Sciences students

Sub-themes

Medical Genomics encompasses 8 sub-themes that highlight key focus areas of LUMC research. Each sub-theme connects the cutting-edge knowledge of multiple research groups led by internationally recognized principal investigators. Medical Genomics research is inherently multidisciplinary. Hence, innovation is virtually always the result of combining concepts, methods and approaches that cut across sub-themes.

Our sub-themes

Genomic Therapeutics (ambassador: Willeke van Roon-Mom)

Our long-term goal is to develop and implement novel RNA and DNA therapeutics. We are already seeing how our increased knowledge from innovative genomics technologies can identify new therapeutic targets and novel therapeutic approaches. Our subtheme aims to facilitate and train scientists that can both develop, apply and translate results from such state of the art genomics methods to the clinic. We aim to integrate disease modelling, target identification and therapy development and align with demands of the regulatory bodies. We will continuously incorporate new platforms and treatment modalities by in-house developments and forging new collaborations.

Pharmacogenomics (ambassador: Jesse Swen)

Everyday a large number of patients receive medications that are, at an individual level, either ineffective or dangerous. Pharmacogenomics aims to improve the outcomes of drug treatment by gaining a better understanding of the genetic mechanisms that result in this inter-individual variability in drug response. Genome science is continuously providing new tools that help to unravel the genetic origin of this variability. By applying cutting-edge genomic technologies available within the medical genomics theme, and trough mechanistic and clinical studies, we aim to improve our ability to predict drug response and deliver personalized medicine to patient care in a wide range of disorders.

Single-cell Genomics (ambassador: Ahmed Mahfouz)

Single-cell genomics have revolutionized our understanding of biological systems by allowing researchers to measure the molecular properties of millions of cells simultaneously. At the LUMC, we use cutting-edge single-cell technologies to map the cellular heterogeneity of complex tissues in humans and model organisms throughout development. Combining these cell maps with advanced machine learning methods, we model how cellular states are perturbed in diseases and how they change after treatment. The single-cell genomics subtheme actively participates in the Single Cell Network Leiden (scNL) to bring together researchers and clinicians with shared interest in single-cell technology, analysis, and application.

Tumor Genomics (ambassador: Danielle Cohen)

In the subtheme tumor-genomics, we aim to determine and understand genetic alterations in individual tumors in order to deliver precision diagnostics and treatment to individual cancer patients. By close collaboration between pathologists, molecular biologists and data scientists, we continuously optimize our (DNA-NGS, RNA-NGS, WGS and Liquid Biopsy) panels according to new molecular targets, seek for new technology to cover molecular changes better and faster, and employ AI for precision diagnosis. Already, NGS techniques found their place in the clinic, where molecular testing is performed on daily basis for the detection of druggable targets, but also to identify rare (subtypes of) tumors. As such, Medical Genomics is closely related to all clinical Tumor Boards of the LUMC, as well as to LUMC’s theme Cancer.

Clinical Genetics (ambassador: Gijs Santen)

In the subtheme clinical genetics we strive to improve our counseling and diagnostic testing for the thousands of patients with rare diseases we see every year. We continuously look for new and better technologies to find causative mutations in established and new disease genes, and improve interpretation for example by data sharing and establishment of episignatures. In the LUMC we focus on several key genetic disorders for which we collect high-quality and often longitudinal data. We use this data to (1) assess the risk for disease development and thus optimize screening programmes, (2) establish genotype-phenotype correlations which improves the information we can give our patients; and (3) prepare for future clinical trials.

Functional Genomics (ambassador: Sylvie Noordermeer)

Despite today’s relative ease to identify (epi)genetic alterations in patients, their functional relationships to disease often remain unclear. In our subtheme functional genomics, we are committed to understand and predict the phenotypical consequences of disease-related genetic alterations. We approach this goal by mimicking the genetic alterations in models ranging from cell lines to patient-derived organoids and animal models. In these systems, we perform genome-wide functional screens, study -omics alterations and use dedicated molecular biology tools to understand the functional consequences of the alterations. For our innovative research, we benefit from the state-of-the-art research infrastructure and the expertise of the technology focus areas within the LUMC. The results of our studies will have important implications for the fundamental understanding of molecular and cellular processes and will have clinical relevance for improving diagnosis and treatment of a multitude of diseases in a future of personalized medicine.

Epigenomics (ambassador: Silvère van der Maarel)

While almost every cell in our body has the same genetic information, they can be phenotypically very different. Indeed, each cell selectively uses relevant genetic information through the epigenetic patterning of its genome. This epigenetic patterning by DNA methylation, by histone use and distribution, and by histone modifications, is developmentally regulated, can be mitotically transmitted and contributes to the regulation of gene expression. It is therefore not surprising that errors in the human epigenome can lead to cellular dysfunction and disease. Within the subtheme Epigenomics we study epigenetic processes in health and disease using state-of-the-art (single cell) technologies in patient cells and model cell systems, iPSC-derived organoids and in animal models to identify, diagnose and understand the epigenetic underpinnings of development and disease. Since epigenetic states are dynamic and responsive to environmental influences, intervention studies are part of our program in an effort to target epigenetic mechanisms of disease.

Population Genomics (ambassador: Bas Heijmans)

Medicine will progressively change from a reactive to a proactive discipline. Population genomics is vital to this transformation by developing the omics-based tools that will enable personalized prevention and early intervention in daily clinical practice. To achieve this goal, we harness state-of-the-art technologies to acquire genomics and other large-scale omics data in complementary population studies, often by collaborating in national and international consortia. Moreover, we apply the full range of data science methods to discover how the interplay between intrinsic biological processes, modifiable lifestyle factors and other environmental exposures shape health across the life course. This will result in biomarkers that can detect excess disease risk of an individual at an early stage and pinpoint the specific disease processes involved to guide precise interventions.