{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T17:41:16Z","timestamp":1790185276576,"version":"4.1.0"},"reference-count":55,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T00:00:00Z","timestamp":1710460800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["SRA#54654"],"award-info":[{"award-number":["SRA#54654"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["J3-50115"],"award-info":[{"award-number":["J3-50115"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["P3-0343"],"award-info":[{"award-number":["P3-0343"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["20200113"],"award-info":[{"award-number":["20200113"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["20230039"],"award-info":[{"award-number":["20230039"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["20210119"],"award-info":[{"award-number":["20210119"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University Medical Centre Ljubljana","award":["SRA#54654"],"award-info":[{"award-number":["SRA#54654"]}]},{"name":"University Medical Centre Ljubljana","award":["J3-50115"],"award-info":[{"award-number":["J3-50115"]}]},{"name":"University Medical Centre Ljubljana","award":["P3-0343"],"award-info":[{"award-number":["P3-0343"]}]},{"name":"University Medical Centre Ljubljana","award":["20200113"],"award-info":[{"award-number":["20200113"]}]},{"name":"University Medical Centre Ljubljana","award":["20230039"],"award-info":[{"award-number":["20230039"]}]},{"name":"University Medical Centre Ljubljana","award":["20210119"],"award-info":[{"award-number":["20210119"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>In this study, we aimed to identify patients within our B-ALL cohort with altered PAX5. Our objective was to use a comprehensive analysis approach to characterize the types of genetic changes, determine their origin (somatic\/germline), and analyze the clinical outcomes associated with them. A consecutive cohort of 99 patients with B-ALL treated at the Children\u2019s Hospital of the UMC Ljubljana according to the ALL IC-BFM 2009 protocol was included in our study. We used RNA sequencing data for gene expression analysis, fusion gene detection and single nucleotide variant identification, multiplex-ligation dependent probe amplification for copy number variation assessment, and Sanger sequencing for germline variant detection. PAX5 was impacted in 33.3% of our patients, with the genetic alterations ranging from CNVs and rearrangements to SNVs. The most common were CNVs, which were found in more than a third of patients, followed by point mutations in 5.2%, and gene rearrangements in 4.1%. We identified eight patients with a PAX5-associated genetic subtype that were previously classified as \u201cB-other\u201d, and they showed intermediate outcomes. We showed higher minimal residual disease values at the end of induction and poorer event-free survival in hyperdiploid cases carrying duplications in PAX5 compared to other hyperdiploid cases. We also report an interesting case of a patient with PAX5::FKBP15 and a pathogenic variant in PTPN11 who underwent an early relapse with a monocytic switch. In conclusion, this study provides valuable insights into the presence, frequency, and prognostic significance of diverse PAX5 alterations in B-ALL patients, highlighting the complexity of genetic factors and their impact on patient outcomes.<\/jats:p>","DOI":"10.3390\/cancers16061164","type":"journal-article","created":{"date-parts":[[2024,3,15]],"date-time":"2024-03-15T12:02:39Z","timestamp":1710504159000},"page":"1164","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["PAX5 Alterations in a Consecutive Childhood B-Cell Acute Lymphoblastic Leukemia Cohort Treated Using the ALL IC-BFM 2009 Protocol"],"prefix":"10.3390","volume":"16","author":[{"given":"Klementina","family":"\u010crepin\u0161ek","sequence":"first","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nika","family":"Klobu\u010dar","sequence":"additional","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0234-2122","authenticated-orcid":false,"given":"Tine","family":"Tesovnik","sequence":"additional","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"\u0160ket","sequence":"additional","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Jenko Bizjan","sequence":"additional","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3080-4838","authenticated-orcid":false,"given":"Jernej","family":"Kova\u010d","sequence":"additional","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marko","family":"Kav\u010di\u010d","sequence":"additional","affiliation":[{"name":"Department of Oncology and Haematology, University Children\u2019s Hospital, University Medical Centre Ljubljana, Bohori\u010deva ulica 20, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toma\u017e","family":"Prelog","sequence":"additional","affiliation":[{"name":"Department of Oncology and Haematology, University Children\u2019s Hospital, University Medical Centre Ljubljana, Bohori\u010deva ulica 20, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lidija","family":"Kitanovski","sequence":"additional","affiliation":[{"name":"Department of Oncology and Haematology, University Children\u2019s Hospital, University Medical Centre Ljubljana, Bohori\u010deva ulica 20, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janez","family":"Jazbec","sequence":"additional","affiliation":[{"name":"Department of Oncology and Haematology, University Children\u2019s Hospital, University Medical Centre Ljubljana, Bohori\u010deva ulica 20, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maru\u0161a","family":"Debeljak","sequence":"additional","affiliation":[{"name":"Clinical Institute for Special Laboratory Diagnostics, University Children\u2019s Hospital, University Medical Centre Ljubljana, Vrazov trg 1, 1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,3,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/ni1454","article-title":"Pax5: The Guardian of B Cell Identity and Function","volume":"8","author":"Cobaleda","year":"2007","journal-title":"Nat. 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