Detecting, classifying, and monitoring CNS tumors with nanopore sequencing

Ann-Kristin Afflerbach, from University Medical Center Hamburg-Eppendorf, introduced nanopore sequencing as a potential method for routine molecular diagnostics of cell-free DNA from cerebrospinal fluid (CSF) supernatants, and Carlo Vermeulen, from UMC Utrecht Center for Molecular Medicine and Oncode Institute, discussed nanopore sequencing for intraoperative tumor classification.

CNS tumor classification during surgery, using nanopore sequencing

The treatment of CNS tumors starts with a surgical resection to reduce tumor mass. The neurosurgeon has to decide between radical resection versus a more conservative strategy to prevent surgical morbidity. The benefit of a radical resection varies between tumor types, and should be limited to those tumors where it is really needed. However due to a lack of pre-operative tissue-based diagnostics, limited knowledge of the precise tumor type is available at the time of surgery.

Meet the speaker

Carlo Vermeulen studied biomedical sciences at the University of Utrecht and did his PhD in the group of Wouter de Laat at the Hubrecht Institute, studying molecular genomics. After his PhD, he started as a postdoc at the University Medical Center in Utrecht in the group of Jeroen de Ridder, to focus on nanopore sequencing and the detection of DNA methylation in cancer.

Classification of brain tumors by nanopore sequencing of cfDNA from CSF

This talk is introducing nanopore sequencing as a potential method for routine molecular diagnostics of cell-free DNA from cerebrospinal fluid (CSF) supernatants. After analyses of >150 samples from patients with a suspected brain tumor, or a history of brain tumors, we show that this method is able to identify diagnostic or prognostic copy number changes. It may further determine the molecular brain tumor class based on an algorithm that compares the global DNA methylation pattern of the cell-free DNA in the CSF with a reference cohort of >2,500 methylation profiles from well characterized brain tumor tissue samples. Our approach is not only able to establish molecular diagnoses for brain tumors that are inaccessible or that don’t need a surgical resection. We also show that nanopore sequencing of CSF is a highly valuable method for tumor monitoring when it comes to the detection of minimal residual disease or the prediction of a tumor relapse.

Meet the speaker

Ann-Kristin Afflerbach studied Molecular Life Sciences at the University of Hamburg. Then went on to study a Molecular Biosciences Masters and has been a PhD candidate at the Research Institute Children’s Cancer Center Hamburg in Prof. Schüller's research group since 2020.