{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T18:45:28Z","timestamp":1769280328785,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008263","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,11,10]],"date-time":"2020-11-10T00:00:00Z","timestamp":1604966400000}}],"reference-count":32,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2020,10,29]],"date-time":"2020-10-29T00:00:00Z","timestamp":1603929600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100001445","name":"Alex's Lemonade Stand Foundation for Childhood Cancer","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100001445","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Medulloblastoma is a highly heterogeneous pediatric brain tumor with five molecular subtypes, Sonic Hedgehog <jats:italic>TP53<\/jats:italic>-mutant, Sonic Hedgehog <jats:italic>TP53<\/jats:italic>-wildtype, WNT, Group 3, and Group 4, defined by the World Health Organization. The current mechanism for classification into these molecular subtypes is through the use of immunostaining, methylation, and\/or genetics. We surveyed the literature and identified a number of RNA-Seq and microarray datasets in order to develop, train, test, and validate a robust classifier to identify medulloblastoma molecular subtypes through the use of transcriptomic profiling data. We have developed a GPL-3 licensed R package and a Shiny Application to enable users to quickly and robustly classify medulloblastoma samples using transcriptomic data. The classifier utilizes a large composite microarray dataset (15 individual datasets), an individual microarray study, and an RNA-Seq dataset, using gene ratios instead of gene expression measures as features for the model. Discriminating features were identified using the limma R package and samples were classified using an unweighted mean of normalized scores. We utilized two training datasets and applied the classifier in 15 separate datasets. We observed a minimum accuracy of 85.71% in the smallest dataset and a maximum of 100% accuracy in four datasets with an overall median accuracy of 97.8% across the 15 datasets, with the majority of misclassification occurring between the heterogeneous Group 3 and Group 4 subtypes. We anticipate this medulloblastoma transcriptomic subtype classifier will be broadly applicable to the cancer research and clinical communities.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008263","type":"journal-article","created":{"date-parts":[[2020,10,29]],"date-time":"2020-10-29T19:01:16Z","timestamp":1603998076000},"page":"e1008263","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["A transcriptome-based classifier to determine molecular subtypes in medulloblastoma"],"prefix":"10.1371","volume":"16","author":[{"given":"Komal S.","family":"Rathi","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9471-3444","authenticated-orcid":true,"given":"Sherjeel","family":"Arif","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3857-6633","authenticated-orcid":true,"given":"Mateusz","family":"Koptyra","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0625-666X","authenticated-orcid":true,"given":"Ammar S.","family":"Naqvi","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3302-4610","authenticated-orcid":true,"given":"Deanne M.","family":"Taylor","sequence":"additional","affiliation":[]},{"given":"Phillip B.","family":"Storm","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0436-4189","authenticated-orcid":true,"given":"Adam C.","family":"Resnick","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2171-3627","authenticated-orcid":true,"given":"Jo Lynne","family":"Rokita","sequence":"additional","affiliation":[]},{"given":"Pichai","family":"Raman","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,10,29]]},"reference":[{"key":"pcbi.1008263.ref001","unstructured":"Medulloblastoma\u2014Childhood\u2014Statistics [Internet]. 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