{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T23:23:50Z","timestamp":1793402630645,"version":"4.5.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,8,25]],"date-time":"2023-08-25T00:00:00Z","timestamp":1692921600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Molecular brain tumor diagnosis is usually dependent on tissue biopsies or resections. This can pose several risks associated with anesthesia or neurosurgery, especially for lesions in the brain stem or other difficult-to-reach anatomical sites. Apart from initial diagnosis, tumor progression, recurrence, or the acquisition of novel genetic alterations can only be proven by re-biopsies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We employed Nanopore sequencing on cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) and analyzed copy number variations (CNV) and global DNA methylation using a random forest classifier. We sequenced 129 samples with sufficient DNA. These samples came from 99 patients and encompassed 22 entities. Results were compared to clinical diagnosis and molecular analysis of tumor tissue, if available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>110\/129 samples were technically successful, and 50 of these contained detectable circulating tumor DNA (ctDNA) by CNV or methylation profiling. ctDNA was detected in samples from patients with progressive disease but also from patients without known residual disease. CNV plots showed diagnostic and prognostic alterations, such as C19MC amplifications in embryonal tumors with multilayered rosettes or Chr.1q gains and Chr.6q losses in posterior fossa group A ependymoma, respectively. Most CNV profiles mirrored the profiles of the respective tumor tissue. DNA methylation allowed exact classification of the tumor in 22\/110 cases and led to incorrect classification in 2\/110 cases. Only 5\/50 samples with detected ctDNA contained tumor cells detectable through microscopy.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our results suggest that Nanopore sequencing data of cfDNA from CSF samples may be a promising approach for initial brain tumor diagnostics and an important tool for disease monitoring.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/clinchem\/hvad115","type":"journal-article","created":{"date-parts":[[2023,7,23]],"date-time":"2023-07-23T08:12:17Z","timestamp":1690099937000},"page":"250-260","source":"Crossref","is-referenced-by-count":78,"title":["Classification of Brain Tumors by Nanopore Sequencing of Cell-Free DNA from Cerebrospinal Fluid"],"prefix":"10.1093","volume":"70","author":[{"given":"Ann-Kristin","family":"Afflerbach","sequence":"first","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]},{"name":"Research Institute Children\u2019s Cancer Center Hamburg , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christian","family":"Rohrandt","sequence":"additional","affiliation":[{"name":"Institute for Communications Technologies and Embedded Systems, University of Applied Sciences Kiel , Kiel ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn","family":"Br\u00e4ndl","sequence":"additional","affiliation":[{"name":"Center for Integrative Psychiatry, University Hospital Schleswig-Holstein , Kiel ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marthe","family":"S\u00f6nksen","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00fcrgen","family":"Hench","sequence":"additional","affiliation":[{"name":"Department of Pathology, University Hospital Basel , Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Frank","sequence":"additional","affiliation":[{"name":"Department of Pathology, University Hospital Basel , Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"B\u00f6rnigen","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malik","family":"Alawi","sequence":"additional","affiliation":[{"name":"Bioinformatics Core, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3302-2719","authenticated-orcid":false,"given":"Martin","family":"Mynarek","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beate","family":"Winkler","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1321-6930","authenticated-orcid":false,"given":"Franz","family":"Ricklefs","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Synowitz","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, University Hospital Schleswig-Holstein, Campus Kiel , Kiel ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lasse","family":"D\u00fchrsen","sequence":"additional","affiliation":[{"name":"Department of Neurosurgery, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Rutkowski","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9394-8519","authenticated-orcid":false,"given":"Annika K","family":"Wefers","sequence":"additional","affiliation":[{"name":"Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]},{"name":"Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg- Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franz-Josef","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"Center for Integrative Psychiatry, University Hospital Schleswig-Holstein , Kiel ,","place":["Germany"]},{"name":"Department of Genome Regulation, Max Planck Institute for Molecular Genetics Berlin , Berlin ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1373-8130","authenticated-orcid":false,"given":"Melanie","family":"Schoof","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]},{"name":"Research Institute Children\u2019s Cancer Center Hamburg , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8731-1121","authenticated-orcid":false,"given":"Ulrich","family":"Sch\u00fcller","sequence":"additional","affiliation":[{"name":"Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]},{"name":"Research Institute Children\u2019s Cancer Center Hamburg , Hamburg ,","place":["Germany"]},{"name":"Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,8,25]]},"reference":[{"key":"2025043019484824300_hvad115-B1","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1093\/neuonc\/noab106","article-title":"The 2021 WHO classification of 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