{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:23:21Z","timestamp":1789190601181,"version":"build-2803163510"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T00:00:00Z","timestamp":1761782400000},"content-version":"vor","delay-in-days":23,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["817811"],"award-info":[{"award-number":["817811"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["771\/21"],"award-info":[{"award-number":["771\/21"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["3120\/22"],"award-info":[{"award-number":["3120\/22"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01HG009190"],"award-info":[{"award-number":["R01HG009190"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004375","name":"Tel Aviv University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004375","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Cancer Biology Research Center at Tel Aviv University"},{"name":"Nevzlin Family Foundation"},{"DOI":"10.13039\/100001698","name":"Israel Cancer Research Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001698","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fight Kids Cancer"},{"name":"Edmond J. Safra Center for Bioinformatics","award":["0603523011"],"award-info":[{"award-number":["0603523011"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Oxford Nanopore Technology (ONT)-based methylation sequencing is emerging as a powerful approach for the rapid and accurate classification of brain tumors, an essential component of precision oncology. However, its broader clinical adoption has been limited by reliance on fresh-frozen (FF) tissue, whereas the vast majority of clinical specimens are formalin-fixed paraffin-embedded (FFPE). In this study, we address this limitation by evaluating the effects of FFPE processing on DNA methylation profiles and introducing a validated protocol for ONT-based classification using DNA extracted directly from pathology-marked regions on stained FFPE slides. This approach enables the targeted selection of tumor-rich areas following histological assessment, thereby improving DNA input quality and tumor content. We demonstrate that even small, low-input samples (\u226525\u00a0ng) can be successfully classified using this method, with high concordance to final integrated neuropathological diagnoses. Our results show that, despite modest methylation loss associated with formalin fixation, classification performance remains robust. Notably, we identify a correlation between methylation degradation and fixation time, supporting a recommendation to limit formalin exposure to\u00a0\u22643\u20134 days when possible. By enabling accurate methylation-based tumor classification from routinely processed, stained FFPE tissue, our protocol integrates seamlessly into existing clinical workflows. This expands the accessibility of ONT-based diagnostics and supports informed, timely treatment decisions\u2014even in cases with minimal tissue availability or urgent clinical need.<\/jats:p>","DOI":"10.1093\/narcan\/zcaf038","type":"journal-article","created":{"date-parts":[[2025,9,28]],"date-time":"2025-09-28T11:47:44Z","timestamp":1759060064000},"source":"Crossref","is-referenced-by-count":2,"title":["Brain tumor classification from FFPE samples using nanopore methylation sequencing"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-4457-3445","authenticated-orcid":false,"given":"Galina","family":"Feinberg-Gorenshtein","sequence":"first","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Assaf","family":"Grunwald","sequence":"additional","affiliation":[{"name":"School of Chemistry, Tel Aviv University Department of Physical Chemistry, ,\u00a0P.O. Box 39040, Tel Aviv,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlo","family":"Vermeulen","sequence":"additional","affiliation":[{"name":"Center for Molecular Medicine, University Medical Center Utrecht , P.O. Box 85500, 3508 GA Utrecht ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nurit Gal","family":"Mark","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]},{"name":"Felsenstein Medical Research Center, Tel Aviv University , Rabin Medical Center (Beilinson Campus), 39 Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Shinderman-Maman","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adva","family":"Levy-Barda","sequence":"additional","affiliation":[{"name":"Rabin Medical Center\u00a0(Beilinson Hospital) Biobank, Department of Pathology, , Attn: Biobank, 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]},{"name":"Holon Institute of Technology Department of Digital Medical Technologies, ,\u00a0P.O. Box 305, Holon,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keren","family":"Shichrur","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal","family":"Hameiri-Grossman","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orli","family":"Michaeli","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]},{"name":"Tel Aviv University, Gray Faculty of Medical and Health Sciences , P.O. Box 39040, Tel Aviv,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shira","family":"Amar","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanna","family":"Fichman","sequence":"additional","affiliation":[{"name":"Beilinson Hospital Institute of Pathology Department of Pathology, , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abraham","family":"Natan","sequence":"additional","affiliation":[{"name":"Beilinson Hospital Institute of Pathology Department of Pathology, , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tali","family":"Siegal","sequence":"additional","affiliation":[{"name":"Tel Aviv University, Gray Faculty of Medical and Health Sciences , P.O. Box 39040, Tel Aviv,","place":["Israel"]},{"name":"Neuro-Oncology Unit,\u00a0Davidoff Cancer Center at Rabin Medical Center , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shlomit","family":"Yust-Katz","sequence":"additional","affiliation":[{"name":"Tel Aviv University, Gray Faculty of Medical and Health Sciences , P.O. Box 39040, Tel Aviv,","place":["Israel"]},{"name":"Neuro-Oncology Unit,\u00a0Davidoff Cancer Center at Rabin Medical Center , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanna","family":"Weiss","sequence":"additional","affiliation":[{"name":"Beilinson Hospital Institute of Pathology Department of Pathology, , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osnat","family":"Konen","sequence":"additional","affiliation":[{"name":"The Institute of Imaging, Schneider Children\u2019s Medical Center of Israel ,\u00a0P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Kershenovich","sequence":"additional","affiliation":[{"name":"Division of Pediatric Neurosurgery, Schneider Children\u2019s Medical Center of Israel ,\u00a0P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew\u00a0A","family":"Kanner","sequence":"additional","affiliation":[{"name":"Beilinson Hospital Institute of Pathology Department of Pathology, , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]},{"name":"Rabin Medical Center Department of Neurosurgery, , 39 Ze\u2019ev Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeroen","family":"de\u00a0Ridder","sequence":"additional","affiliation":[{"name":"Center for Molecular Medicine, University Medical Center Utrecht , P.O. Box 85500, 3508 GA Utrecht ,","place":["The Netherlands"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helen","family":"Toledano","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]},{"name":"Tel Aviv University, Gray Faculty of Medical and Health Sciences , P.O. Box 39040, Tel Aviv,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shai","family":"Izraeli","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]},{"name":"Felsenstein Medical Research Center, Tel Aviv University , Rabin Medical Center (Beilinson Campus), 39 Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yehudit","family":"Birger","sequence":"additional","affiliation":[{"name":"The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children\u2019s Medical Center of Israel , P.O. Box 559,\u00a0 Petach Tikva ,","place":["Israel"]},{"name":"Felsenstein Medical Research Center, Tel Aviv University , Rabin Medical Center (Beilinson Campus), 39 Jabotinsky Street, Petah Tikva 4941492 ,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuval","family":"Ebenstein","sequence":"additional","affiliation":[{"name":"School of Chemistry, Tel Aviv University Department of Physical Chemistry, ,\u00a0P.O. Box 39040, Tel Aviv,","place":["Israel"]},{"name":"Sagol School of Neuroscience, Tel Aviv University , P.O. 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