{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:13:54Z","timestamp":1761005634917,"version":"build-2065373602"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T00:00:00Z","timestamp":1746144000000},"content-version":"vor","delay-in-days":31,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The determination of the mutational status in the immunoglobulin variable region is an established prognostic biomarker for chronic lymphocytic leukemia (CLL). The length and inner variability of the variable, diversity, and joining (VDJ) rearranged sequences compromise B-cell clone characterization using next-generation sequencing (NGS), and a standardization is needed to adapt the procedure to the current clinical guidelines. Here, we develop a complete strategy for sequencing the variable domain of the immunoglobulin heavy chain (IGH) locus with a simple, low-cost, and efficient method that enables sequencing using shorter reads (MiSeq 150 \u00d7 2), allowing for faster results. Clonality and mutational status determination are performed within the same analysis pipeline. We tested and validated the method using 319 CLL patients previously diagnosed with IGH locus characterized using Sanger sequencing, along with 47 healthy donor samples. The analysis method follows a clone-centered consensus sequence strategy to identify B-cell clones and establish a clonal threshold specific for each patient\u2019s clonality profile, thereby overcoming the limitations of Sanger sequencing which is the gold standard used for determining immunoglobulin heavy variable (IGHV) mutational status.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf041","type":"journal-article","created":{"date-parts":[[2025,5,2]],"date-time":"2025-05-02T11:47:14Z","timestamp":1746186434000},"source":"Crossref","is-referenced-by-count":0,"title":["Characterization of Chronic Lymphocytic Leukemia Immunoglobulin Rearrangements from Partial Read Sequencing"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2889-9498","authenticated-orcid":false,"given":"Azahara","family":"Fuentes-Trillo","sequence":"first","affiliation":[{"name":"Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3392-4336","authenticated-orcid":false,"given":"Alicia","family":"Serrano-Alcal\u00e1","sequence":"additional","affiliation":[{"name":"Hematology Service, Valencia University Clinical Hospital , Valencia 46010,","place":["Spain"]},{"name":"Physiology Department, University of Valencia , Valencia 46010,","place":["Spain"]},{"name":"Lymphoproliferative Syndrome Group, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9452-7310","authenticated-orcid":false,"given":"Blanca","family":"Ferrer-Lores","sequence":"additional","affiliation":[{"name":"Hematology Service, Valencia University Clinical Hospital , Valencia 46010,","place":["Spain"]},{"name":"Lymphoproliferative Syndrome Group, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7232-0252","authenticated-orcid":false,"given":"Laura","family":"Ventura-L\u00f3pez","sequence":"additional","affiliation":[{"name":"Hematology Service, Valencia University Clinical Hospital , Valencia 46010,","place":["Spain"]},{"name":"Lymphoproliferative Syndrome Group, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5801-1752","authenticated-orcid":false,"given":"Enrique","family":"Seda","sequence":"additional","affiliation":[{"name":"Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2162-6606","authenticated-orcid":false,"given":"Ana-B\u00e1rbara","family":"Garc\u00eda-Garc\u00eda","sequence":"additional","affiliation":[{"name":"Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]},{"name":"CIBERDEM, ISCIII , Madrid 28029,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3313-2654","authenticated-orcid":false,"given":"Blanca","family":"Navarro","sequence":"additional","affiliation":[{"name":"Hematology Service, Valencia University Clinical Hospital , Valencia 46010,","place":["Spain"]},{"name":"INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9467-932X","authenticated-orcid":false,"given":"Mar\u00eda Jos\u00e9","family":"Terol","sequence":"additional","affiliation":[{"name":"Hematology Service, Valencia University Clinical Hospital , Valencia 46010,","place":["Spain"]},{"name":"Lymphoproliferative Syndrome Group, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]},{"name":"Medicine Department, University of Valencia , Valencia 46010,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8009-3689","authenticated-orcid":false,"given":"Felipe Javier","family":"Chaves","sequence":"additional","affiliation":[{"name":"Genomic and Diabetes Unit, INCLIVA Biomedical Research Institute , Valencia 46010,","place":["Spain"]},{"name":"CIBERDEM, ISCIII , Madrid 28029,","place":["Spain"]}]}],"member":"286","published-online":{"date-parts":[[2025,5,2]]},"reference":[{"key":"2025102002020353500_qzaf041-B1","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a035220","article-title":"Chronic lymphocytic leukemia","volume":"11","author":"Chiorazzi","year":"2021","journal-title":"Cold Spring Harb Perspect Med"},{"key":"2025102002020353500_qzaf041-B2","doi-asserted-by":"crossref","first-page":"1848","DOI":"10.1182\/blood.V94.6.1848","article-title":"Unmutated Ig V genes are associated with a more aggressive form of chronic lymphocytic leukemia","volume":"94","author":"Hamblin","year":"1999","journal-title":"Blood"},{"key":"2025102002020353500_qzaf041-B3","doi-asserted-by":"crossref","first-page":"1840","DOI":"10.1182\/blood.V94.6.1840","article-title":"Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia","volume":"94","author":"Damle","year":"1999","journal-title":"Blood"},{"key":"2025102002020353500_qzaf041-B4","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.autrev.2007.02.014","article-title":"From normal to clonal B cells: chronic lymphocytic leukemia (CLL) at the crossroad between neoplasia and autoimmunity","volume":"7","author":"Ghia","year":"2007","journal-title":"Autoimmun Rev"},{"key":"2025102002020353500_qzaf041-B5","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1182\/blood-2017-09-806398","article-title":"iwCLL guidelines for diagnosis, indications for treatment, response assessment, and supportive management of CLL","volume":"131","author":"Hallek","year":"2018","journal-title":"Blood"},{"key":"2025102002020353500_qzaf041-B6","doi-asserted-by":"crossref","first-page":"1961","DOI":"10.1038\/s41375-022-01604-2","article-title":"Immunoglobulin gene sequence analysis in chronic lymphocytic leukemia: the 2022 update of the recommendations by ERIC, the European Research Initiative on CLL","volume":"36","author":"Agathangelidis","year":"2022","journal-title":"Leukemia"},{"key":"2025102002020353500_qzaf041-B7","doi-asserted-by":"crossref","first-page":"1477","DOI":"10.1038\/leu.2017.125","article-title":"Immunoglobulin gene sequence analysis in chronic lymphocytic leukemia: updated ERIC recommendations","volume":"31","author":"Rosenquist","year":"2017","journal-title":"Leukemia"},{"key":"2025102002020353500_qzaf041-B8","doi-asserted-by":"crossref","first-page":"3765","DOI":"10.4049\/jimmunol.1602050","article-title":"High-throughput immunogenetics for clinical and research applications in immunohematology: potential and challenges","volume":"198","author":"Langerak","year":"2017","journal-title":"J Immunol"},{"key":"2025102002020353500_qzaf041-B9","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1038\/leu.2016.307","article-title":"Targeted deep sequencing reveals clinically relevant subclonal IgHV rearrangements in chronic lymphocytic leukemia","volume":"31","author":"Stamatopoulos","year":"2017","journal-title":"Leukemia"},{"key":"2025102002020353500_qzaf041-B10","doi-asserted-by":"crossref","first-page":"2545","DOI":"10.1038\/s41375-020-0923-9","article-title":"Immunoglobulin gene analysis in chronic lymphocytic leukemia in the era of next generation sequencing","volume":"34","author":"Davi","year":"2020","journal-title":"Leukemia"},{"key":"2025102002020353500_qzaf041-B11","doi-asserted-by":"crossref","first-page":"4322","DOI":"10.1073\/pnas.1503587112","article-title":"Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia","volume":"112","author":"Blachly","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025102002020353500_qzaf041-B12","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/j.jmoldx.2014.11.006","article-title":"High-throughput sequencing using the Ion Torrent personal genome machine for clinical evaluation of somatic hypermutation status in chronic lymphocytic leukemia","volume":"17","author":"McClure","year":"2015","journal-title":"J Mol Diagn"},{"key":"2025102002020353500_qzaf041-B13","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.exphem.2020.09.194","article-title":"Reading the B-cell receptor immunome in chronic lymphocytic leukemia: revelations and applications","volume":"93","author":"Hengeveld","year":"2021","journal-title":"Exp 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