ArticleJournal of neuro-oncology2024
Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens.
Article in Journal of neuro-oncology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- The emerging role of intraoperative nanopore sequencing on the neurosurgical strategy in paediatric embryonal brain tumours.Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2026Review
- Feasibility of long-read nanopore sequencing for methylation-based classification of posterior fossa ependymomas.Brain tumor pathology · 2026Article
- Prospective, multicenter validation of a platform for rapid molecular profiling of central nervous system tumors.Nature medicine · 2025Article
- Paired blood and brain tissue methylation biomarkers in focal cortical dysplasia.Brain communications · 2025Article
- Detection of diagnostic somatic copy number alterations from cerebrospinal fluid cell-free DNA in brain tumor patients.Acta neuropathologica communications · 2024Article
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11 authors.
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Abstract
backgroundAlthough 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.
methodsUltrasonic 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.
results19 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.
conclusionMethylation-based classification of pediatric CNS tumors based on ultrasonic aspirator-reduced and otherwise discarded tissue is feasible using time- and cost-efficient nanopore sequencing.
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