Simultaneous methylation and fusion detection for pediatric tumor characterization

Abstract

In pediatric oncology, establishing a precise diagnosis is crucial to identify patients in need of care such as chemotherapy or craniospinal irradiation for brain tumors but also to refine prognosis, as these treatments often lead to adverse neurological effects in a young and growing population. The emergence of nanopore sequencing as a new sequencing technology offers a potential way to refine this diagnosis, through tumor methylation analysis or detection of genetic alterations (fusions, complex rearrangements) driving tumorigenesis. Our study focused on the characterization of twenty pediatric brain tumors and sarcomas. DNA extracted from these tumors was prepared in half a day, then sequenced on a MinION Flow Cell for 48 hours. Enrichment of genomic regions of interest was performed using Oxford Nanopore Technologies’ adaptive sampling method, based on a bed file containing fusion genes of diagnostic relevance. Downstream bioinformatics analysis was conducted using the NanoClid pipeline, developed by our laboratory's bioinformatics team and available on GitHub. Our study shows how nanopore sequencing has revolutionized analysis of pediatric brain tumors and sarcomas. Through this innovative adaptive sampling technique arises a lightning-fast three-in-one tool. For distinct histological types and tumor locations, it has enabled classification through methylation analysis and fusion detection typical of the detected class (YAP1–MAMLD1 fusion in ependymoma, EWSR1–ERG fusion in Ewing's sarcoma, or BRAF–KIAA1549 fusion in pilocytic astrocytoma). This singular approach adeptly unravels methylation profiles, copy number variations, and fusions in brain tumors and sarcomas, offering a complete tool for tumor characterization in a shorter timeframe.

Biography

Dr. Mathilde Filser is a resident in molecular biology, currently working in the somatic department at the Curie Institute in Paris. She has spent her research year working on the potential of nanopore methylation sequencing for the classification of brain tumors. Mathilde is now in her last year of residency at the Curie Institute and keeps working on this amazing topic. She is planning to work in the hospital-university field in Parisian hospitals, to combine routine practice with research.