{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T01:17:30Z","timestamp":1792027050991,"version":"4.4.0"},"reference-count":52,"publisher":"American Society of Clinical Oncology (ASCO)","issue":"6","content-domain":{"domain":["ascopubs.org"],"crossmark-restriction":true},"short-container-title":["JCO Precision Oncology"],"published-print":{"date-parts":[[2022,5]]},"abstract":"<jats:sec><jats:title>PURPOSE<\/jats:title><jats:p> Most cases of pediatric acute leukemia occur in low- and middle-income countries, where health centers lack the tools required for accurate diagnosis and disease classification. Recent research shows the robustness of using unbiased short-read RNA sequencing to classify genomic subtypes of acute leukemia. Compared with short-read sequencing, nanopore sequencing has low capital and consumable costs, making it suitable for use in locations with limited health infrastructure. <\/jats:p><\/jats:sec><jats:sec><jats:title>MATERIALS AND METHODS<\/jats:title><jats:p> We show the feasibility of nanopore mRNA sequencing on 134 cryopreserved acute leukemia specimens (26 acute myeloid leukemia [AML], 73 B-lineage acute lymphoblastic leukemia [B-ALL], 34 T-lineage acute lymphoblastic leukemia, and one acute undifferentiated leukemia). Using multiple library preparation approaches, we generated long-read transcripts for each sample. We developed a novel composite classification approach to predict acute leukemia lineage and major B-ALL and AML molecular subtypes directly from gene expression profiles. <\/jats:p><\/jats:sec><jats:sec><jats:title>RESULTS<\/jats:title><jats:p> We demonstrate accurate classification of acute leukemia samples into AML, B-ALL, or T-lineage acute lymphoblastic leukemia (96.2% of cases are classifiable with a probability of &gt; 0.8, with 100% accuracy) and further classification into clinically actionable genomic subtypes using shallow RNA nanopore sequencing, with 96.2% accuracy for major AML subtypes and 94.1% accuracy for major B-lineage acute lymphoblastic leukemia subtypes. <\/jats:p><\/jats:sec><jats:sec><jats:title>CONCLUSION<\/jats:title><jats:p> Transcriptional profiling of acute leukemia samples using nanopore technology for diagnostic classification is feasible and accurate, which has the potential to improve the accuracy of cancer diagnosis in low-resource settings. <\/jats:p><\/jats:sec>","DOI":"10.1200\/po.21.00326","type":"journal-article","created":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T19:59:20Z","timestamp":1650484760000},"update-policy":"https:\/\/doi.org\/10.1200\/crossmark","source":"Crossref","is-referenced-by-count":18,"title":["Acute Leukemia Classification Using Transcriptional Profiles From Low-Cost Nanopore mRNA Sequencing"],"prefix":"10.1200","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0673-9418","authenticated-orcid":false,"given":"Jeremy","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Genetics, University of North Carolina, Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5282-7833","authenticated-orcid":false,"given":"Nickhill","family":"Bhakta","sequence":"additional","affiliation":[{"name":"Department of Global Pediatric Medicine, St Jude Children's Research Hospital, Memphis, TN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7614-1959","authenticated-orcid":false,"given":"Vanessa","family":"Ayer Miller","sequence":"additional","affiliation":[{"name":"Office of Clinical Translational Research, University of North Carolina, Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahler","family":"Revsine","sequence":"additional","affiliation":[{"name":"Department of Biology, University of North Carolina, Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9816-6302","authenticated-orcid":false,"given":"Mark R.","family":"Litzow","sequence":"additional","affiliation":[{"name":"Division of Hematology and Transplant Center, Mayo Clinic Rochester, Rochester, MN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth","family":"Paietta","sequence":"additional","affiliation":[{"name":"Department of Oncology, Montefiore Medical Center, Bronx, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuri","family":"Fedoriw","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn G.","family":"Roberts","sequence":"additional","affiliation":[{"name":"Department of Pathology, St Jude Children's Research Hospital, Memphis, TN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1581-1327","authenticated-orcid":false,"given":"Zhaohui","family":"Gu","sequence":"additional","affiliation":[{"name":"Department of Computational and Quantitative Medicine & Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1871-1850","authenticated-orcid":false,"given":"Charles G.","family":"Mullighan","sequence":"additional","affiliation":[{"name":"Department of Pathology, St Jude Children's Research Hospital, Memphis, TN"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7281-7130","authenticated-orcid":false,"given":"Corbin D.","family":"Jones","sequence":"additional","affiliation":[{"name":"Department of Biology, University of North Carolina, Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0484-1574","authenticated-orcid":false,"given":"Thomas B.","family":"Alexander","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC"},{"name":"Department of Pediatrics, University of North Carolina, Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"233","reference":[{"key":"b1","volume-title":"Cancer: Disease Control Priorities","volume":"3","author":"Bray F","year":"2015","edition":"2"},{"key":"b2","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(18)30761-7"},{"key":"b3","doi-asserted-by":"publisher","DOI":"10.3322\/caac.21492"},{"key":"b4","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(18)30909-4"},{"key":"b5","doi-asserted-by":"publisher","DOI":"10.1186\/s13045-020-00908-z"},{"key":"b6","first-page":"1","volume":"4","author":"Makau-Barasa LK","year":"2018","journal-title":"JCO Glob Oncol"},{"key":"b7","first-page":"1","volume":"4","author":"Rubagumya F","year":"2018","journal-title":"JCO Glob Oncol"},{"key":"b8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0089102"},{"key":"b9","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2016-03-643544"},{"key":"b10","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2016.70.7836"},{"key":"b11","doi-asserted-by":"publisher","DOI":"10.1111\/ijlh.13135"},{"key":"b12","first-page":"e28087","author":"Bansal D","year":"2019","journal-title":"Pediatr Blood Cancer"},{"key":"b13","doi-asserted-by":"publisher","DOI":"10.1093\/ajcp\/aqx108"},{"key":"b14","doi-asserted-by":"publisher","DOI":"10.1002\/pbc.25583"},{"key":"b15","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(08)70339-5"},{"key":"b16","doi-asserted-by":"publisher","DOI":"10.1016\/S1535-6108(02)00018-1"},{"key":"b17","doi-asserted-by":"publisher","DOI":"10.1126\/science.286.5439.531"},{"key":"b18","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0315-5"},{"key":"b19","doi-asserted-by":"publisher","DOI":"10.1016\/S1535-6108(02)00032-6"},{"key":"b20","doi-asserted-by":"publisher","DOI":"10.1007\/s10549-011-1619-7"},{"key":"b21","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3398"},{"key":"b22","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa0808253"},{"key":"b23","doi-asserted-by":"publisher","DOI":"10.1158\/1940-6207.CAPR-17-0368"},{"key":"b24","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.1000307"},{"key":"b25","doi-asserted-by":"publisher","DOI":"10.1038\/s41375-020-0762-8"},{"key":"b26","volume-title":"WHO Global Initiative for Childhood Cancer: An Overview"},{"key":"b27","doi-asserted-by":"publisher","DOI":"10.1038\/srep31602"},{"key":"b28","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2018.08.003"},{"key":"b29","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-07207-4"},{"key":"b30","first-page":"2825","volume":"12","author":"Pedregosa F","year":"2011","journal-title":"J Mach Learn Res"},{"key":"b31","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-253"},{"key":"b32","doi-asserted-by":"publisher","DOI":"10.1613\/jair.953"},{"key":"b33","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-20-1230"},{"key":"b34","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2287"},{"key":"b35","doi-asserted-by":"publisher","DOI":"10.1038\/nature10725"},{"key":"b36","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1403088"},{"key":"b37","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3909"},{"key":"b38","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-06485-7"},{"key":"b39","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.082099299"},{"key":"b40","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0436-0"},{"key":"b41","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2141.2004.04948.x"},{"key":"b42","doi-asserted-by":"publisher","DOI":"10.1038\/ng.2532"},{"key":"b43","doi-asserted-by":"publisher","DOI":"10.1182\/bloodadvances.2019001008"},{"key":"b44","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa031046"},{"key":"b45","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa040465"},{"key":"b46","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-18-1897"},{"key":"b47","doi-asserted-by":"publisher","DOI":"10.1038\/leu.2016.267"},{"key":"b48","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.22834"},{"key":"b49","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2019.08.008"},{"key":"b50","doi-asserted-by":"publisher","DOI":"10.1039\/C7LC00273D"},{"key":"b51","doi-asserted-by":"publisher","DOI":"10.1039\/C9AN00532C"},{"key":"b52","doi-asserted-by":"publisher","DOI":"10.1182\/bloodadvances.2021004347"}],"container-title":["JCO Precision Oncology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/ascopubs.org\/doi\/pdfdirect\/10.1200\/PO.21.00326","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,29]],"date-time":"2022-05-29T11:02:56Z","timestamp":1653822176000},"score":1,"resource":{"primary":{"URL":"https:\/\/ascopubs.org\/doi\/10.1200\/PO.21.00326"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5]]},"references-count":52,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022,5]]}},"alternative-id":["10.1200\/PO.21.00326"],"URL":"https:\/\/doi.org\/10.1200\/po.21.00326","relation":{},"ISSN":["2473-4284"],"issn-type":[{"value":"2473-4284","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5]]},"assertion":[{"value":"2021-07-19","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-02-03","order":1,"name":"revised","label":"Revised","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-03-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-04-20","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2100326"}}