{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T14:53:45Z","timestamp":1786632825290,"version":"build-2736575974"},"reference-count":14,"publisher":"Wiley","issue":"15","license":[{"start":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:00:00Z","timestamp":1780876800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:00:00Z","timestamp":1780876800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Clinical Laboratory Analysis"],"published-print":{"date-parts":[[2026,8]]},"abstract":"ABSTRACT<\/jats:title>\n \n Background<\/jats:title>\n \n Activating mutations in\n NOTCH1<\/jats:italic>\n are frequent in T\u2010cell acute lymphoblastic leukemia (T\u2010ALL) and, in the absence of alterations in RAS or PTEN, are associated with favorable prognosis. Besides classical heterodimerization and PEST domain mutations, juxtamembrane internal tandem duplications (JME\u2010ITDs) represent a third class of activating variants. Their intermediate size and sequence composition can challenge short\u2010read next\u2010generation sequencing and variant calling algorithms, leading to underdetection in routine diagnostics.\n <\/jats:p>\n <\/jats:sec>\n \n Methods<\/jats:title>\n \n An index case of newly diagnosed T\u2010ALL harboring a\n NOTCH1<\/jats:italic>\n juxtamembrane insertion that was discordantly detected by variant callers during routine targeted NGS (Hematology OncoKitDx v2) prompted further analysis. The variant was evaluated using VarDict and VarScan2, followed by manual inspection with IGV and orthogonal confirmation by Sanger sequencing. To further assess variability in the detection of JME\u2010ITDs, six additional BAM files from patients with previously confirmed variants were reanalyzed using VarDict, VarScan2, Mutect2, and Pindel.\n <\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n \n In the index case, VarDict detected a 51\u2010bp\n NOTCH1<\/jats:italic>\n JME\u2010ITD (c.5168\u20102_5216dup) that was missed by VarScan2 and confirmed by Sanger sequencing. Reanalysis of the seven cases showed that Mutect2 and VarDict detected all JME\u2010ITDs (100%), VarScan2 identified only three (42.8%), and Pindel detected six mutations (85.7%). These results reflect differences in algorithmic strategies where haplotype\u2010based callers incorporate soft\u2010clipped and split reads, whereas pileup\u2010based discard them.\n <\/jats:p>\n <\/jats:sec>\n \n Conclusion<\/jats:title>\n \n Detection of\n NOTCH1<\/jats:italic>\n JME\u2010ITDs depends strongly on variant\u2010calling strategy. Combining haplotype\u2010based callers with split\u2010read structural variant tools may reduce false negatives and improve detection of clinically relevant insertions in diagnostic NGS pipelines.\n <\/jats:p>\n <\/jats:sec>","DOI":"10.1002\/jcla.70279","type":"journal-article","created":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T12:32:05Z","timestamp":1780921925000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Not Missing the Notch: Detection Challenges of Juxtamembrane\n \n NOTCH1<\/i>\n <\/scp>\n Variant Detection in T\u2010Cell Acute Lymphoblastic Leukemia"],"prefix":"10.1002","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9907-0556","authenticated-orcid":false,"given":"Francisco","family":"Beas","sequence":"first","affiliation":[{"name":"Department of Hematology, Hospital Universitari Vall D'hebron (HUVH), experimental Hematology, Vall D'hebron Institute of Oncology (VHIO), Department of Medicine Universitat Aut\u00f2noma de Barcelona Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2432-8898","authenticated-orcid":false,"given":"Stephan","family":"Hutter","sequence":"additional","affiliation":[{"name":"MLL Munich Leukemia Laboratory Munich Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ferran","family":"Balbastre\u2010\u00dabeda","sequence":"additional","affiliation":[{"name":"Department of Hematology, Hospital Universitari Vall D'hebron (HUVH), experimental Hematology, Vall D'hebron Institute of Oncology (VHIO), Department of Medicine Universitat Aut\u00f2noma de Barcelona Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Novoa\u2010J\u00e1uregui","sequence":"additional","affiliation":[{"name":"Department of Hematology, Hospital Universitari Vall D'hebron (HUVH), experimental Hematology, Vall D'hebron Institute of Oncology (VHIO), Department of Medicine Universitat Aut\u00f2noma de Barcelona Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Gabarr\u00f3s\u2010Subir\u00e0","sequence":"additional","affiliation":[{"name":"Department of Hematology, Hospital Universitari Vall D'hebron (HUVH), experimental Hematology, Vall D'hebron Institute of Oncology (VHIO), Department of Medicine Universitat Aut\u00f2noma de Barcelona Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eulalia","family":"Genesc\u00e0","sequence":"additional","affiliation":[{"name":"Institut D'investigaci\u00f3 Contra la Leucemia Josep Carreras (IJC), campus ICO\u2010Germans Trias i Pujol Universitat Aut\u00f2noma de Barcelona Badalona Spain Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petri","family":"P\u00f6l\u00f6nen","sequence":"additional","affiliation":[{"name":"St. Jude Children's Research Hospital Memphis Tennessee USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torsten","family":"Haferlach","sequence":"additional","affiliation":[{"name":"MLL Munich Leukemia Laboratory Munich Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s","family":"Jerez","sequence":"additional","affiliation":[{"name":"Department of Hematology, Hospital Universitari Vall D'hebron (HUVH), experimental Hematology, Vall D'hebron Institute of Oncology (VHIO), Department of Medicine Universitat Aut\u00f2noma de Barcelona Barcelona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,6,8]]},"reference":[{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood.2023023568"},{"key":"e_1_2_5_3_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood.2023020794"},{"key":"e_1_2_5_4_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2007-12-130096"},{"key":"e_1_2_5_5_1","doi-asserted-by":"publisher","DOI":"10.1182\/asheducation-2009.1.353"},{"key":"e_1_2_5_6_1","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2008-10-184069"},{"key":"e_1_2_5_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1527"},{"key":"e_1_2_5_8_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-016-1031-8"},{"key":"e_1_2_5_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2021.07.012"},{"key":"e_1_2_5_10_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep43169"},{"key":"e_1_2_5_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw227"},{"key":"e_1_2_5_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2514"},{"key":"e_1_2_5_13_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.129684.111"},{"key":"e_1_2_5_14_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp394"},{"key":"e_1_2_5_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07807-0"}],"container-title":["Journal of Clinical Laboratory Analysis"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcla.70279","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jcla.70279","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jcla.70279","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T14:22:54Z","timestamp":1786630974000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcla.70279"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,8]]},"references-count":14,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2026,8]]}},"alternative-id":["10.1002\/jcla.70279"],"URL":"https:\/\/doi.org\/10.1002\/jcla.70279","archive":["Portico"],"relation":{},"ISSN":["0887-8013","1098-2825"],"issn-type":[{"value":"0887-8013","type":"print"},{"value":"1098-2825","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,8]]},"assertion":[{"value":"2026-03-11","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-28","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-08","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70279"}}