In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in paediatric oncology in a cost-effective and minimally invasive manner.

Cancer Research Institute Ghent Ghent Belgium

Center for Medical Biotechnology Flemish Institute Biotechnology Ghent Belgium

Department of Biomolecular Medicine Ghent University Ghent Belgium

Department of Pediatric Hematology and Oncology Charles University Prague 2nd Faculty of Medicine and University Hospital Motol Prague Czech Republic

Department of Pediatric Hematology Oncology and Stem Cell Transplantation Ghent University Hospital Ghent Belgium

INSERM U830 Laboratoire de Génétique et Biologie des Cancers Research Center Institut Curie Paris France

Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands

SiRIC RTOP « Recherche Translationelle En Oncologie Pédiatrique » Institut Curie Paris France

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