Clinical Research Program – Diagnostics

Clinical program director: Dr. Bastiaan Tops

Program topics

Whole Genome Sequencing (WGS)

With Whole Genome Sequencing (WGS) as a standard test within healthcare, we can map the whole genome of the tumor, allowing detection of all genomic abnormalities in one analysis. This method not only provides valuable insights for initial diagnosis, but also opens up additional possibilities in the areas of pharmacogenetics, HLA typing and personalized treatments. WGS also enables individualized patient follow-up during treatment by using patient-specific genetic abnormalities in the tumor. This allows techniques such as liquid biopsies and minimal residual disease (MRD) diagnostics to fine-tune treatment and monitor disease progress in real time.

Tumor classification using methylation profiling

The epigenetic pattern is often unique to different tumor types and thus can be used tumor classification. We are using nanopore sequencing in combination with AI models to provide rapid and accurate diagnoses. For tumors of the central nervous system (CNS), we have already developed a model, Sturgeon, that allows diagnosis to be determined during surgery, allowing the surgeon to immediately adjust surgical management. We are currently extending this technology to solid tumors and leukemia, with the goal of providing faster and more accurate diagnostics. In time, we hope this will facilitate new treatment options and clinical trials, contributing to better care for cancer patients.

Nanopore sequencing

Nanopore sequencing is a promising technology that we are currently using for methylation profiling and tumor classification (see above). Our research focuses on expanding this technique to detect all genetic abnormalities in tumors with a single test. This would be a huge step forward, as it both simplifies and accelerates diagnostics. In addition, nanopore sequencing requires significantly fewer resources than traditional methods, making it particularly suitable for countries with limited resources. By making this technology more accessible, we aim to “democratize” diagnostics for children with cancer and reduce global health inequalities.

Innovative Diagnostic Technologies

In addition to genomic and epigenetic analyses, we are exploring several innovative technologies to further improve pediatric cancer diagnostics. We are developing new applications within flow cytometry, not only for hematological malignancies but also for solid tumors, enabling faster and more accurate analysis of cell populations. In addition, we are betting on multiplex immunohistochemistry and spatial proteomics to map the tumor environment and protein expression in detail. Image analysis of pathology images, supported by artificial intelligence, provides additional opportunities to recognize patterns faster and refine diagnoses. By combining these technologies with our other initiatives, such as whole genome sequencing and methylation profiling, we aim to provide comprehensive and efficient diagnostics with the ultimate goal of providing the very best diagnostics for every child with cancer.