{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T04:36:10Z","timestamp":1787027770738,"version":"build-2736575974"},"reference-count":41,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T00:00:00Z","timestamp":1591660800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["IG 2014 n. 16105"],"award-info":[{"award-number":["IG 2014 n. 16105"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cancers"],"abstract":"<jats:p>The monitoring of minimal residual disease (MRD) in Philadelphia-negative acute lymphoblastic leukemia (ALL) requires the identification at diagnosis of immunoglobulin\/T-cell receptor (Ig\/TCR) rearrangements as clonality markers. Aiming to simplify and possibly improve the patients\u2019 initial screening, we designed a capture-based next-generation sequencing (NGS) panel combining the Ig\/TCR rearrangement detection with the profiling of relevant leukemia-related genes. The validation of the assay on well-characterized samples allowed us to identify all the known Ig\/TCR rearrangements as well as additional clonalities, including rare rearrangements characterized by uncommon combinations of variable, diversity, and joining (V-D-J) gene segments, oligoclonal rearrangements, and low represented clones. Upon validation, the capture NGS approach allowed us to identify Ig\/TCR clonal markers in 87% of a retrospective cohort (MRD-unknown within the Northern Italy Leukemia Group (NILG)-ALL 09\/00 clinical trial) and in 83% of newly-diagnosed ALL cases in which conventional method failed, thus proving its prospective applicability. Finally, we identified gene variants in 94.7% of patients analyzed for mutational status with the same implemented capture assay. The prospective application of this technology could simplify clonality assessment and improve standard assay development for leukemia monitoring, as well as provide information about the mutational status of selected leukemia-related genes, potentially representing new prognostic elements, MRD markers, and targets for specific therapies.<\/jats:p>","DOI":"10.3390\/cancers12061505","type":"journal-article","created":{"date-parts":[[2020,6,9]],"date-time":"2020-06-09T08:49:11Z","timestamp":1591692551000},"page":"1505","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Capture-Based Next-Generation Sequencing Improves the Identification of Immunoglobulin\/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4353-2210","authenticated-orcid":false,"given":"Roberta","family":"Cavagna","sequence":"first","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"},{"name":"Department of Pathophysiology and Transplantation, Universit\u00e0 degli Studi di Milano, 20122 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie L.","family":"Guinea Montalvo","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuela","family":"Tosi","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michela","family":"Paris","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5767-8942","authenticated-orcid":false,"given":"Chiara","family":"Pavoni","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tamara","family":"Intermesoli","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8214-2894","authenticated-orcid":false,"given":"Renato","family":"Bassan","sequence":"additional","affiliation":[{"name":"Hematology Unit, dell\u2019Angelo Hospital and SS. Giovanni and Paolo Hospital, 30174 Venezia Mestre, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Mosca","sequence":"additional","affiliation":[{"name":"Department of Pathophysiology and Transplantation, Universit\u00e0 degli Studi di Milano, 20122 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3739-7502","authenticated-orcid":false,"given":"Alessandro","family":"Rambaldi","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"},{"name":"Department of Oncology and Hematology, Universit\u00e0 degli Studi di Milano, 20122 Milano, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0374-1536","authenticated-orcid":false,"given":"Orietta","family":"Spinelli","sequence":"additional","affiliation":[{"name":"Hematology and Bone Marrow Transplant Unit, Azienda Socio-Sanitaria Territoriale (ASST) Papa Giovanni XXIII, 24127 Bergamo, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,6,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1056\/NEJM199808273390904","article-title":"Clinical significance of minimal residual disease in childhood acute lymphoblastic leukemia. 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