{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T13:21:35Z","timestamp":1774444895393,"version":"3.50.1"},"reference-count":31,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"funder":[{"DOI":"10.13039\/501100000950","name":"Cancer Council South Australia","doi-asserted-by":"publisher","award":["APP1156283"],"award-info":[{"award-number":["APP1156283"]}],"id":[{"id":"10.13039\/501100000950","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1117718"],"award-info":[{"award-number":["APP1117718"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1027531"],"award-info":[{"award-number":["APP1027531"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","award":["APP1135949"],"award-info":[{"award-number":["APP1135949"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020541","name":"Royal Adelaide Hospital Research Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020541","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100020670","name":"Cancer Council Australia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100020670","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014152","name":"Ray and Shirl Norman Cancer Research Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100014152","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100022513","name":"Tasmanian Department of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100022513","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","jmdjournal.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["The Journal of Molecular Diagnostics"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.jmoldx.2025.09.003","type":"journal-article","created":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:51:17Z","timestamp":1760140277000},"page":"39-52","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Enhanced Detection of Splice-Altering Variants in Hematologic Malignancies Using Targeted RNA-Sequencing Data"],"prefix":"10.1016","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6526-9762","authenticated-orcid":false,"given":"Muneeza","family":"Maqsood","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5135-6504","authenticated-orcid":false,"given":"John","family":"Toubia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7705-1146","authenticated-orcid":false,"given":"Carol","family":"Wadham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5895-8797","authenticated-orcid":false,"given":"Naranie","family":"Shanmuganathan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nur Hezrin","family":"Shahrin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5375-9334","authenticated-orcid":false,"given":"Adelina","family":"Fernandes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6645-971X","authenticated-orcid":false,"given":"Joe","family":"McConnell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2795-9927","authenticated-orcid":false,"given":"Verity","family":"Saunders","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9205-1934","authenticated-orcid":false,"given":"Dominik","family":"Kaczorowski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosalie R.","family":"Kenyon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Timothy P.","family":"Hughes","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3181-7852","authenticated-orcid":false,"given":"Chung Hoow","family":"Kok","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5095-7981","authenticated-orcid":false,"given":"Susan","family":"Branford","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.jmoldx.2025.09.003_bib1","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1038\/s41467-019-09374-9","article-title":"Diagnosis of fusion genes using targeted RNA sequencing","volume":"10","author":"Heyer","year":"2019","journal-title":"Nat Commun"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib2","doi-asserted-by":"crossref","first-page":"297","DOI":"10.3324\/haematol.2018.203133","article-title":"Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia","volume":"104","author":"Dillon","year":"2019","journal-title":"Haematologica"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib3","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1093\/clinchem\/hvaa221","article-title":"Targeted RNA-sequencing enables detection of relevant translocations and single nucleotide variants and provides a method for classification of hematological malignancies-RANKING","volume":"66","author":"de Lange","year":"2020","journal-title":"Clin Chem"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib4","doi-asserted-by":"crossref","DOI":"10.1097\/HS9.0000000000000522","article-title":"Performances of targeted RNA sequencing for the analysis of fusion transcripts, gene mutation, and expression in hematological malignancies","volume":"5","author":"Hayette","year":"2021","journal-title":"Hemasphere"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib5","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1016\/j.jmoldx.2021.05.008","article-title":"Diagnostic validation of a clinical laboratory-oriented targeted RNA sequencing system for detecting gene fusions in hematologic malignancies","volume":"23","author":"Lim","year":"2021","journal-title":"J Mol Diagn"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib6","first-page":"2380","article-title":"Impact of additional genetic abnormalities at diagnosis of chronic myeloid leukemia for first-line imatinib-treated patients receiving proactive treatment intervention","volume":"108","author":"Shanmuganathan","year":"2023","journal-title":"Haematologica"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib7","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1182\/bloodadvances.2022009179","article-title":"Classification and genetics of pediatric B-other acute lymphoblastic leukemia by targeted RNA sequencing","volume":"7","author":"Migita","year":"2023","journal-title":"Blood Adv"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib8","doi-asserted-by":"crossref","first-page":"4394","DOI":"10.3390\/cancers15174394","article-title":"Expanding the clinical utility of targeted RNA sequencing panels beyond gene fusions to complex, intragenic structural rearrangements","volume":"15","author":"Schieffer","year":"2023","journal-title":"Cancers (Basel)"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib9","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.jmoldx.2023.09.013","article-title":"Transcriptome sequencing allows comprehensive genomic characterization of pediatric b-acute lymphoblastic leukemia in an academic clinical laboratory","volume":"26","author":"Hu","year":"2024","journal-title":"J Mol Diagn"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib10","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aal5209","article-title":"Improving genetic diagnosis in Mendelian disease with transcriptome sequencing","volume":"9","author":"Cummings","year":"2017","journal-title":"Sci Transl Med"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib11","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1182\/blood-2018-02-832253","article-title":"Integrative Genomic Analysis reveals cancer-associated mutations at diagnosis of CML in patients with high-risk disease","volume":"132","author":"Branford","year":"2018","journal-title":"Blood"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib12","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1016\/j.jmoldx.2022.04.004","article-title":"RNA-based targeted gene sequencing improves the diagnostic yield of mutant detection in chronic myeloid leukemia","volume":"24","author":"Shanmuganathan","year":"2022","journal-title":"J Mol Diagn"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib13","doi-asserted-by":"crossref","first-page":"2051","DOI":"10.1038\/s41375-020-0751-y","article-title":"Aberrant RAG-mediated recombination contributes to multiple structural rearrangements in lymphoid blast crisis of chronic myeloid leukemia","volume":"34","author":"Thomson","year":"2020","journal-title":"Leukemia"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib14","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/ng.2874","article-title":"RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia","volume":"46","author":"Papaemmanuil","year":"2014","journal-title":"Nat Genet"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib15","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/nature05690","article-title":"Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia","volume":"446","author":"Mullighan","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib16","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1038\/nature06866","article-title":"BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros","volume":"453","author":"Mullighan","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib17","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/s13045-020-00972-5","article-title":"The specific distribution pattern of IKZF1 mutation in acute myeloid leukemia","volume":"13","author":"Zhang","year":"2020","journal-title":"J Hematol Oncol"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib18","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib19","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nbt.2024","article-title":"Targeted RNA sequencing reveals the deep complexity of the human transcriptome","volume":"30","author":"Mercer","year":"2011","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib20","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","article-title":"Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications","volume":"32","author":"Chen","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib21","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1101\/gr.257246.119","article-title":"Accurate and efficient detection of gene fusions from RNA sequencing data","volume":"31","author":"Uhrig","year":"2021","journal-title":"Genome Res"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib22","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s13059-019-1842-9","article-title":"Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods","volume":"20","author":"Haas","year":"2019","journal-title":"Genome Biol"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib23","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/s41467-020-20573-7","article-title":"Detection of aberrant splicing events in RNA-seq data using FRASER","volume":"12","author":"Mertes","year":"2021","journal-title":"Nat Commun"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib24","doi-asserted-by":"crossref","first-page":"3014","DOI":"10.1093\/bioinformatics\/btab152","article-title":"Megadepth: efficient coverage quantification for BigWigs and BAMs","volume":"37","author":"Wilks","year":"2021","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib25","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/ng.2653","article-title":"The Genotype-Tissue Expression (GTEx) project","volume":"45","author":"Lonsdale","year":"2013","journal-title":"Nat Genet"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib26","doi-asserted-by":"crossref","first-page":"D733","DOI":"10.1093\/nar\/gkv1189","article-title":"Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation","volume":"44","author":"O'Leary","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib27","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1002\/j.1538-7305.1948.tb01338.x","article-title":"A mathematical theory of communication","volume":"27","author":"Shannon","year":"1948","journal-title":"Bell Syst Tech J"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib28","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.1056\/NEJMoa1312542","article-title":"Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2","volume":"369","author":"Nangalia","year":"2013","journal-title":"N Engl J Med"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib29","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1002\/sim.2993","article-title":"Youden Index and the optimal threshold for markers with mass at zero","volume":"27","author":"Schisterman","year":"2008","journal-title":"Stat Med"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib30","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"10.1016\/j.jmoldx.2025.09.003_bib31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v098.i11","article-title":"cutpointr: Improved estimation and validation of optimal cutpoints in R","volume":"98","author":"Thiele","year":"2021","journal-title":"J Stat Softw"}],"updated-by":[{"DOI":"10.1016\/j.jmoldx.2026.01.006","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2026,2,11]],"date-time":"2026-02-11T00:00:00Z","timestamp":1770768000000}},{"DOI":"10.1016\/j.jmoldx.2026.01.006","type":"erratum","label":"Erratum","source":"publisher","updated":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T00:00:00Z","timestamp":1775001600000}}],"container-title":["The Journal of Molecular Diagnostics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1525157825002387?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1525157825002387?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T04:55:54Z","timestamp":1773896154000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1525157825002387"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1]]}},"alternative-id":["S1525157825002387"],"URL":"https:\/\/doi.org\/10.1016\/j.jmoldx.2025.09.003","relation":{},"ISSN":["1525-1578"],"issn-type":[{"value":"1525-1578","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Enhanced Detection of Splice-Altering Variants in Hematologic Malignancies Using Targeted RNA-Sequencing Data","name":"articletitle","label":"Article Title"},{"value":"The Journal of Molecular Diagnostics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jmoldx.2025.09.003","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Crown Copyright \u00a9 2026 Published by Elsevier Inc. on behalf of the Association for Molecular Pathology and American Society for Investigative Pathology. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}