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- Title
Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens.
- Authors
Simon, Michèle; Kuschel, Luis P.; von Hoff, Katja; Yuan, Dongsheng; Hernáiz Driever, Pablo; Hain, Elisabeth G.; Koch, Arend; Capper, David; Schulz, Matthias; Thomale, Ulrich-Wilhelm; Euskirchen, Philipp
- Abstract
Background: Although cavitating ultrasonic aspirators are commonly used in neurosurgical procedures, the suitability of ultrasonic aspirator-derived tumor material for diagnostic procedures is still controversial. Here, we explore the feasibility of using ultrasonic aspirator-resected tumor tissue to classify otherwise discarded sample material by fast DNA methylation-based analysis using low pass nanopore whole genome sequencing. Methods: Ultrasonic aspirator-derived specimens from pediatric patients undergoing brain tumor resection were subjected to low-pass nanopore whole genome sequencing. DNA methylation-based classification using a neural network classifier and copy number variation analysis were performed. Tumor purity was estimated from copy number profiles. Results were compared to microarray (EPIC)-based routine neuropathological histomorphological and molecular evaluation. Results: 19 samples with confirmed neuropathological diagnosis were evaluated. All samples were successfully sequenced and passed quality control for further analysis. DNA and sequencing characteristics from ultrasonic aspirator-derived specimens were comparable to routinely processed tumor tissue. Classification of both methods was concordant regarding methylation class in 17/19 (89%) cases. Application of a platform-specific threshold for nanopore-based classification ensured a specificity of 100%, whereas sensitivity was 79%. Copy number variation profiles were generated for all cases and matched EPIC results in 18/19 (95%) samples, even allowing the identification of diagnostically or therapeutically relevant genomic alterations. Conclusion: Methylation-based classification of pediatric CNS tumors based on ultrasonic aspirator-reduced and otherwise discarded tissue is feasible using time- and cost-efficient nanopore sequencing.
- Subjects
BRAIN tumors; DNA analysis; WHOLE genome sequencing; ULTRASONICS; SHOTGUN sequencing; EPIGENOMICS; CHILD patients; DEMETHYLATION; ASPIRATORS
- Publication
Journal of Neuro-Oncology, 2024, Vol 169, Issue 1, p73
- ISSN
0167-594X
- Publication type
Article
- DOI
10.1007/s11060-024-04702-6