{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T04:47:08Z","timestamp":1770958028259,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T00:00:00Z","timestamp":1727136000000},"content-version":"vor","delay-in-days":84,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"France G\u00e9nomique National infrastructure"},{"name":"Agence Nationale pour la Recherche (ANR) projet HEMASEQ - France G\u00e9nomique","award":["ANR-10-INSB-09"],"award-info":[{"award-number":["ANR-10-INSB-09"]}]},{"name":"le Canc\u00e9rop\u00f4le GrandSud-Ouest","award":["2017-EM24"],"award-info":[{"award-number":["2017-EM24"]}]},{"name":"ANR : Transipedia","award":["ANR-18-CE45-0020"],"award-info":[{"award-number":["ANR-18-CE45-0020"]}]},{"name":"full-RNA","award":["ANR-22-CE45-0007"],"award-info":[{"award-number":["ANR-22-CE45-0007"]}]},{"DOI":"10.13039\/501100004431","name":"La Fondation de France","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004431","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA sequencing technology combining short read and long read analysis can be used to detect chimeric RNAs in malignant cells. Here, we propose an integrated approach that uses k-mers to analyze indexed datasets. This approach is used to identify chimeric RNA in chronic myelomonocytic leukemia (CMML) cells, a myeloid malignancy that associates features of myelodysplastic and myeloproliferative neoplasms. In virtually every CMML patient, new generation sequencing identifies one or several somatic driver mutations, typically affecting epigenetic, splicing and signaling genes. In contrast, cytogenetic aberrations are currently detected in only one third of the cases. Nevertheless, chromosomal abnormalities contribute to patient stratification, some of them being associated with higher risk of poor outcome, e.g. through transformation into acute myeloid leukemia (AML). Our approach selects four chimeric RNAs that have been detected and validated in CMML cells. We further focus on NRIP1-MIR99AHG, as this fusion has also recently been detected in AML cells. We show that this fusion encodes three isoforms, including a novel one. Further studies will decipher the biological significance of such a fusion and its potential to improve disease stratification. Taken together, this report demonstrates the ability of a large-scale approach to detect chimeric RNAs in cancer cells.<\/jats:p>","DOI":"10.1093\/nargab\/lqae117","type":"journal-article","created":{"date-parts":[[2024,9,24]],"date-time":"2024-09-24T12:55:36Z","timestamp":1727182536000},"source":"Crossref","is-referenced-by-count":1,"title":["Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq"],"prefix":"10.1093","volume":"6","author":[{"given":"Florence","family":"Ruffl\u00e9","sequence":"first","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00e9r\u00f4me","family":"Reboul","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anthony","family":"Boureux","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Benoit","family":"Guibert","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chlo\u00e9","family":"Bessi\u00e8re","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"},{"name":"CRCT, Inserm, CNRS, University Toulouse III-Paul Sabatier , 31100\u00a0 Toulouse , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raissa","family":"Silva","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Jourdan","sequence":"additional","affiliation":[{"name":"Department of Hematology, N\u00eemes University Hospital , 30900\u00a0 N\u00eemes , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Baptiste","family":"Gaillard","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Cytogenomics, Montpellier university hospital , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anne","family":"Boland","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, Centre National de Recherche en G\u00e9nomique Humaine , 91057\u00a0 Evry , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Fran\u00e7ois","family":"Deleuze","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, CEA, Centre National de Recherche en G\u00e9nomique Humaine , 91057\u00a0 Evry , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine","family":"S\u00e9namaud-Beaufort","sequence":"additional","affiliation":[{"name":"GenomiqueENS, Institut de Biologie de l\u2019ENS (IBENS), D\u00e9partement de biologie, \u00c9cole normale sup\u00e9rieure, CNRS, INSERM, Universit\u00e9 PSL , 75005\u00a0 Paris , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Doroth\u00e9e","family":"Selimoglu-Buet","sequence":"additional","affiliation":[{"name":"Department of Hematology, Gustave Roussy Cancer Center, Universit\u00e9 Paris-Saclay , 94805 Villejuif , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Solary","sequence":"additional","affiliation":[{"name":"Department of Hematology, Gustave Roussy Cancer Center, Universit\u00e9 Paris-Saclay , 94805 Villejuif , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3311-7494","authenticated-orcid":false,"given":"Nicolas","family":"Gilbert","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7918-0176","authenticated-orcid":false,"given":"Th\u00e9r\u00e8se","family":"Commes","sequence":"additional","affiliation":[{"name":"IRMB, University of Montpellier, INSERM , 80 rue Augustin Fliche , 34295\u00a0 Montpellier , France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,9,24]]},"reference":[{"key":"2024092410460458800_B1","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/s41408-018-0148-6","article-title":"Challenges in the introduction of next-generation sequencing (NGS) for 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