{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T15:49:02Z","timestamp":1766159342481,"version":"3.41.2"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T00:00:00Z","timestamp":1705363200000},"content-version":"vor","delay-in-days":15,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000015","name":"Canadian Cancer Society Research Institute","doi-asserted-by":"publisher","award":["705056"],"award-info":[{"award-number":["705056"]}],"id":[{"id":"10.13039\/501100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000015","name":"Canadian Cancer Society Research Institute","doi-asserted-by":"publisher","award":["409302"],"award-info":[{"award-number":["409302"]}],"id":[{"id":"10.13039\/501100000015","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Tali\u2019s Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Despite genomic simplicity, recent studies have reported at least 3 major atypical teratoid rhabdoid tumor (ATRT) subgroups with distinct molecular and clinical features. Reliable ATRT subgrouping in clinical settings remains challenging due to a lack of suitable biological markers, sample rarity, and the relatively high cost of conventional subgrouping methods. This study aimed to develop a reliable ATRT molecular stratification method to implement in clinical settings.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We have developed an ATRT subgroup predictor assay using a custom genes panel for the NanoString nCounter System and a flexible machine learning classifier package. Seventy-one ATRT primary tumors with matching gene expression array and NanoString data were used to construct a multi-algorithms ensemble classifier. Additional validation was performed using an independent gene expression array against the independently generated dataset. We also analyzed 11 extra-cranial rhabdoid tumors with our classifier and compared our approach against DNA methylation classification to evaluate the result consistency with existing methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have demonstrated that our novel ensemble classifier has an overall average of 93.6% accuracy in the validation dataset, and a striking 98.9% accuracy was achieved with the high-prediction score samples. Using our classifier, all analyzed extra-cranial rhabdoid tumors are classified as MYC subgroups. Compared with the DNA methylation classification, the results show high agreement, with 84.5% concordance and up to 95.8% concordance for high-confidence predictions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Here we present a rapid, cost-effective, and accurate ATRT subgrouping assay applicable for clinical use.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/noajnl\/vdae004","type":"journal-article","created":{"date-parts":[[2024,1,16]],"date-time":"2024-01-16T18:42:27Z","timestamp":1705430547000},"source":"Crossref","is-referenced-by-count":1,"title":["Rapid, economical diagnostic classification of ATRT molecular subgroup using NanoString nCounter platform"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3322-5604","authenticated-orcid":false,"given":"Ben","family":"Ho","sequence":"first","affiliation":[{"name":"Division of Cell Biology, The Hospital for Sick Children , Toronto, Ontario , Canada"},{"name":"Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children , Toronto, Ontario , Canada"},{"name":"Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Arnoldo","sequence":"additional","affiliation":[{"name":"Division of Pathology, Hospital for Sick Children , Toronto, Ontario , Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yvonne","family":"Zhong","sequence":"additional","affiliation":[{"name":"Division of Pathology, Hospital for Sick Children , Toronto, Ontario , Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mei","family":"Lu","sequence":"additional","affiliation":[{"name":"Division of Cell Biology, The Hospital for Sick Children , Toronto, Ontario , Canada"},{"name":"Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children , Toronto, Ontario , Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathon","family":"Torchia","sequence":"additional","affiliation":[{"name":"Cantata Bio, LLC , Scott\u2019s Valley, California , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fupan","family":"Yao","sequence":"additional","affiliation":[{"name":"Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children , Toronto, Ontario , Canada"},{"name":"Department of Medical Biophysics, Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2618-4402","authenticated-orcid":false,"given":"Cynthia","family":"Hawkins","sequence":"additional","affiliation":[{"name":"Division of Cell Biology, The Hospital for Sick Children , Toronto, Ontario , Canada"},{"name":"Arthur and Sonia 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