{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T18:33:13Z","timestamp":1780597993402,"version":"3.54.1"},"reference-count":28,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012524","name":"American Lebanese Syrian Associated Charities","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012524","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["P30 CA021765"],"award-info":[{"award-number":["P30 CA021765"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Brain Pathology"],"published-print":{"date-parts":[[2025,9]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>DNA methylation profiling by Illumina methylation array\u2010based methods has revolutionized the molecular classification and diagnosis of brain tumors. A significant barrier to adopting these methods in a clinical environment is the requirement for specialized scanners, which results in high additional costs and a larger laboratory footprint. DNA sequencing\u2010based alternatives are attractive because most clinical molecular pathology laboratories already use sequencers for other molecular assays. This study aimed to compare the utility of the newly developed sequencing\u2010based enzymatic methyl sequencing (EM\u2010seq) method paired with the Twist Human Methylome panel for brain tumor classification with standard Infinium Methylation BeadChip\u2010based methods. We used DNA from fresh\u2010frozen or formalin\u2010fixed, paraffin\u2010embedded (FFPE) brain cancer samples from 19 patients and 1 control sample to construct DNA libraries covering 3.98 million CpG sites. We developed and validated a bioinformatics pipeline to analyze target\u2010enriched EM\u2010seq (TEEM\u2010seq) data in comparison with standard array\u2010based methods for tumor classification and copy number profiling. We found high concordance between TEEM\u2010seq and traditional methods, with high correlation coefficients (&gt;0.98) between FFPE replicates. We successfully classified tumor samples into the expected molecular classes with robust prediction scores (&gt;0.82). We observed that FFPE samples required a sequencing depth of at least 35x to achieve consistently high and reliable prediction scores. The TEEM\u2010seq method has the potential to complement existing tumor classification methods and lower the barriers for the adoption of methylation profiling in routine clinical use.<\/jats:p>","DOI":"10.1111\/bpa.70000","type":"journal-article","created":{"date-parts":[[2025,3,7]],"date-time":"2025-03-07T22:23:32Z","timestamp":1741386212000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Validation of target\u2010enriched enzymatic methylation sequencing for brain tumor classification from formalin\u2010fixed paraffin embedded\u2010derived <scp>DNA<\/scp>"],"prefix":"10.1111","volume":"35","author":[{"given":"Quynh T.","family":"Tran","sequence":"first","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sujuan","family":"Jia","sequence":"additional","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"},{"name":"Clinical Biomarker Laboratory St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Md. Zahangir","family":"Alom","sequence":"additional","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles G.","family":"Mullighan","sequence":"additional","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"},{"name":"Clinical Biomarker Laboratory St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth G.","family":"Tatevossian","sequence":"additional","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"},{"name":"Clinical Biomarker Laboratory St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0997-4728","authenticated-orcid":false,"given":"Brent A.","family":"Orr","sequence":"additional","affiliation":[{"name":"Department of Pathology St. Jude Children's Research Hospital  Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,2,28]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(16)30297-2"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-31827-x"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12935-023-03074-7"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature26000"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20603-4"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13148-021-01085-7"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-013-1126-5"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1080\/15592294.2022.2051861"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3270"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1158\/1055-9965.EPI-14-0464"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0214368"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ygeno.2020.07.032"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22973"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1080\/15592294.2015.1132136"},{"key":"e_1_2_11_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40478-024-01728-9"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/nan.12856"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06615-2"},{"key":"e_1_2_11_19_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17091579"},{"key":"e_1_2_11_20_1","first-page":"2579","article-title":"Visualizing Data using t\u2010SNE","volume":"9","author":"Maaten L","year":"2008","journal-title":"J Mach Learn Res"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41698-024-00718-3"},{"key":"e_1_2_11_22_1","unstructured":"HovestadtVZM.Conumee: enhanced copy\u2010number variation analysis using Illumina methylation arrays v.1.4.2 R package v.0.99.4.2015."},{"key":"e_1_2_11_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.prnil.2023.01.001"},{"key":"e_1_2_11_24_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0282672"},{"key":"e_1_2_11_25_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.266551.120"},{"key":"e_1_2_11_26_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-35959-6"},{"key":"e_1_2_11_27_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-52114-3"},{"key":"e_1_2_11_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature13268"},{"key":"e_1_2_11_29_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-024-02731-z"}],"container-title":["Brain Pathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/bpa.70000","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T23:48:32Z","timestamp":1755215312000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/bpa.70000"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,28]]},"references-count":28,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2025,9]]}},"alternative-id":["10.1111\/bpa.70000"],"URL":"https:\/\/doi.org\/10.1111\/bpa.70000","archive":["Portico"],"relation":{},"ISSN":["1015-6305","1750-3639"],"issn-type":[{"value":"1015-6305","type":"print"},{"value":"1750-3639","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,28]]},"assertion":[{"value":"2024-11-24","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-02-03","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-02-28","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70000"}}