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Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens

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Názov: Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens
Autori: Michèle Simon, Luis P. Kuschel, Katja von Hoff, Dongsheng Yuan, Pablo Hernáiz Driever, Elisabeth G. Hain, Arend Koch, David Capper, Matthias Schulz, Ulrich-Wilhelm Thomale, Philipp Euskirchen
Zdroj: J Neurooncol
Simon, M, Kuschel, L P, von Hoff, K, Yuan, D, Hernáiz Driever, P, Hain, E G, Koch, A, Capper, D, Schulz, M, Thomale, U W & Euskirchen, P 2024, 'Rapid DNA methylation-based classification of pediatric brain tumors from ultrasonic aspirate specimens', Journal of Neuro-Oncology, vol. 169, no. 1, pp. 73-83. https://doi.org/10.1007/s11060-024-04702-6
Informácie o vydavateľovi: Springer Science and Business Media LLC, 2023.
Rok vydania: 2023
Predmety: Male, Nanopore sequencing, DNA Copy Number Variations, Adolescent, Whole Genome Sequencing, Brain Neoplasms, Research, Infant, DNA Methylation, 3. Good health, Ultrasonic aspirator, Child, Preschool, Pediatric brain cancer, Humans, Female, Child, Adolescent [MeSH], Female [MeSH], Brain Neoplasms/genetics [MeSH], Humans [MeSH], Whole Genome Sequencing/methods [MeSH], DNA Copy Number Variations [MeSH], Infant [MeSH], Male [MeSH], Brain Neoplasms/classification [MeSH], DNA Methylation [MeSH], Child [MeSH], Child, Preschool [MeSH], Brain Neoplasms/pathology [MeSH]
Popis: 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.
Druh dokumentu: Article
Other literature type
Jazyk: English
ISSN: 1573-7373
0167-594X
DOI: 10.1007/s11060-024-04702-6
DOI: 10.1101/2023.10.25.23297418
Prístupová URL adresa: https://pubmed.ncbi.nlm.nih.gov/38769169
https://repository.publisso.de/resource/frl:6517544
https://pure.au.dk/portal/en/publications/5032c49e-973d-41f6-a49f-695f3039fc34
https://doi.org/10.1007/s11060-024-04702-6
http://www.scopus.com/inward/record.url?scp=85193594941&partnerID=8YFLogxK
Rights: CC BY
Prístupové číslo: edsair.doi.dedup.....b7ca665a6adc4c3dddb7f0492134f6b1
Databáza: OpenAIRE
Popis
Abstrakt: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.
ISSN:15737373
0167594X
DOI:10.1007/s11060-024-04702-6