{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T02:19:30Z","timestamp":1792808370069,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,18]]},"group-title":"Cancer Biology","reference-count":96,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Alex's Lemonade Stand Foundation (ALSF) Young Investigator Awards","id":[{"id":"https:\/\/ror.org\/038ja4880","id-type":"ROR","asserted-by":"crossref"}]},{"name":"American Society of Clinical Oncology (ASCO) Career Development Award","id":[{"id":"https:\/\/ror.org\/02xjhr934","id-type":"ROR","asserted-by":"crossref"}]},{"name":"ASCO-Conquer Cancer Sarcoma Foundation of America YIA","id":[{"id":"https:\/\/ror.org\/022tv3h63","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Boston Children\u2019s Hospital (BCH) Translational Research Program Mentored Translational Investigator Service Award","id":[{"id":"https:\/\/ror.org\/00dvg7y05","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Dana-Farber Cancer Institute (DFCI) Wong Family Award in Translational Oncology","id":[{"id":"https:\/\/ror.org\/02jzgtq86","id-type":"ROR","asserted-by":"crossref"}]},{"name":"DFCI-BCH Pedals for Pediatrics grant"},{"name":"Rally Foundation Career Development Award","id":[{"id":"https:\/\/ror.org\/02xjhr934","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Sarcoma Foundation of America Jay Vernon Jackson Memorial Research Award","id":[{"id":"https:\/\/ror.org\/022tv3h63","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Department of Defense Peer-Reviewed Cancer Research Program Fellow Career Development Award","award":["CA220721"],"award-info":[{"award-number":["CA220721"]}],"id":[{"id":"https:\/\/ror.org\/02xjhr934","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Break Through Cancer\u2019s Defying Osteosarcoma Project","id":[{"id":"https:\/\/ror.org\/00a8me616","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Count Me In\u2019s Osteosarcoma Project"},{"name":"Boehringer Ingelheim Fonds MD Fellowship","id":[{"id":"https:\/\/ror.org\/00dkye506","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institutes of Health","award":["U2CCA252974"],"award-info":[{"award-number":["U2CCA252974"]}]},{"name":"National Institutes of Health","award":["K08CA276701"],"award-info":[{"award-number":["K08CA276701"]}]},{"name":"National Institutes of Health","award":["5U2CCA252974-06"],"award-info":[{"award-number":["5U2CCA252974-06"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The genomic landscape of osteosarcoma, the most common bone cancer worldwide, is among the most structurally complex of all human malignancies. The identification of recurrent and functionally consequential patterns has thus remained a challenge. Across 236 whole-genome sequencing osteosarcoma samples, we uncovered five genomic hotspots of clustered structural variation collectively altered in 58% of tumors. Four were associated with amplification of oncogenes (\n                  <jats:italic>MYC<\/jats:italic>\n                  ,\n                  <jats:italic>CCND3<\/jats:italic>\n                  ,\n                  <jats:italic>CCNE1<\/jats:italic>\n                  ,\n                  <jats:italic>CDK4)<\/jats:italic>\n                  , while the fifth mapped largely upstream of\n                  <jats:italic>TP53<\/jats:italic>\n                  . Hotspot events showed coordinated patterns of co-occurrence and mutual exclusivity with each other and with tumor suppressor alterations, suggesting genomic context-specific selection. We found localized transcriptional dysregulation at hotspot event loci, and single cells harboring these events converged on a neural crest-like program, linking these structural alterations to a less differentiated cell state. These events were also detectable non-invasively through liquid biopsies and displayed ongoing structural evolution throughout disease progression, a finding with potential clinical utility. Our results provide novel insight into how complex rearrangements shape oncogenesis in osteosarcoma, with broader relevance to other cancers characterized by complex genomes.\n                <\/jats:p>","DOI":"10.64898\/2026.09.14.751472","type":"posted-content","created":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T15:35:24Z","timestamp":1789745724000},"source":"Crossref","is-referenced-by-count":0,"title":["Clustered structural variant hotspots enable oncogenic addiction and plasticity in osteosarcoma"],"prefix":"10.64898","author":[{"given":"Shreya","family":"Raman","sequence":"first","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thorsten","family":"Kaltenbacher","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Merrell","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kavya","family":"Prasad","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-1060-7065","authenticated-orcid":false,"given":"Yutaro","family":"Tanaka","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob","family":"Weiss","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Iannetta","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Byron","family":"Butaney","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Jorswieck","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Faculty of Medicine, Heidelberg University, Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amr","family":"Salem","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lorena","family":"Lazo De La Vega","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evelina","family":"Ceca","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julia M.W.","family":"Wong","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suzanne J.","family":"Forrest","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Klega","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammad","family":"Tanhaemami","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cora A.","family":"Ricker","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Stomatology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diane M.","family":"Diehl","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeremy","family":"Johnson","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carrie","family":"Cibulskis","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristy","family":"Schlueter-Kuck","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liam Q.","family":"Alley","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Boston Children\u2019s Hospital, Boston, MA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2980-9244","authenticated-orcid":false,"given":"Natalie B.","family":"Collins","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8825-7158","authenticated-orcid":false,"given":"Cheng-Zhong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Pathology, Harvard Medical School, Boston, MA, USA"},{"name":"Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA"},{"name":"National Cancer Institute, National Institutes of Health, Bethesda, MD, USA"},{"name":"Howard Hughes Medical Institute, Chevy Chase, MD, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David S.","family":"Shulman","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian D.","family":"Crompton","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine A.","family":"Janeway","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gad","family":"Getz","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Harvard Medical School, Boston, MA, USA"},{"name":"Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Riaz","family":"Gillani","sequence":"additional","affiliation":[{"name":"Dana-Farber\/Boston Children\u2019s Cancer and Blood Disorders Center, Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard, Cambridge, MA, USA"},{"name":"Department of Pediatrics, Harvard Medical School, Boston, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092210251333000_2026.09.14.751472v1.1","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1038\/s41572-022-00409-y","article-title":"Osteosarcoma","volume":"8","year":"2022","journal-title":"Nat. Rev. Dis. Primer"},{"key":"2026092210251333000_2026.09.14.751472v1.2","doi-asserted-by":"publisher","DOI":"10.1002\/pbc.24429"},{"key":"2026092210251333000_2026.09.14.751472v1.3","doi-asserted-by":"publisher","DOI":"10.1200\/JCO.2003.03.141"},{"key":"2026092210251333000_2026.09.14.751472v1.4","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMRA2103423\/SUPPL_FILE\/NEJMRA2103423_DISCLOSURES.PDF"},{"key":"2026092210251333000_2026.09.14.751472v1.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2014.03.003"},{"key":"2026092210251333000_2026.09.14.751472v1.6","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1016\/j.ccell.2026.02.012","article-title":"The landscape of structural variation in pediatric cancer","volume":"44","year":"2026","journal-title":"Cancer Cell"},{"key":"2026092210251333000_2026.09.14.751472v1.7","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.12.005"},{"key":"2026092210251333000_2026.09.14.751472v1.8","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms15936"},{"key":"2026092210251333000_2026.09.14.751472v1.9","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.23253"},{"key":"2026092210251333000_2026.09.14.751472v1.10","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-20-1230"},{"key":"2026092210251333000_2026.09.14.751472v1.11","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1419260111"},{"key":"2026092210251333000_2026.09.14.751472v1.12","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-1969-6"},{"key":"2026092210251333000_2026.09.14.751472v1.13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-14646-w"},{"key":"2026092210251333000_2026.09.14.751472v1.14","doi-asserted-by":"publisher","DOI":"10.64898\/2026.06.10.731352"},{"key":"2026092210251333000_2026.09.14.751472v1.15","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv710"},{"key":"2026092210251333000_2026.09.14.751472v1.16","doi-asserted-by":"publisher","DOI":"10.1101\/gr.221028.117"},{"key":"2026092210251333000_2026.09.14.751472v1.17","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-1965-x"},{"key":"2026092210251333000_2026.09.14.751472v1.18","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s43018-020-0027-5","article-title":"A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies","volume":"1","year":"2020","journal-title":"Nat. Cancer"},{"key":"2026092210251333000_2026.09.14.751472v1.19","doi-asserted-by":"publisher","DOI":"10.1038\/nature17676"},{"key":"2026092210251333000_2026.09.14.751472v1.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-03064-z"},{"key":"2026092210251333000_2026.09.14.751472v1.21","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-08107-3"},{"key":"2026092210251333000_2026.09.14.751472v1.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0576-7"},{"key":"2026092210251333000_2026.09.14.751472v1.23","doi-asserted-by":"crossref","unstructured":"Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).","DOI":"10.1038\/s41467-018-08200-y"},{"key":"2026092210251333000_2026.09.14.751472v1.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.04.004"},{"key":"2026092210251333000_2026.09.14.751472v1.25","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0564-y"},{"key":"2026092210251333000_2026.09.14.751472v1.26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002772"},{"key":"2026092210251333000_2026.09.14.751472v1.27","doi-asserted-by":"crossref","unstructured":"Pellarin, I. et al. Cyclin-dependent protein kinases and cell cycle regulation in biology and disease. Signal Transduct. Target. Ther. 10, 11 (2025).","DOI":"10.1038\/s41392-024-02080-z"},{"key":"2026092210251333000_2026.09.14.751472v1.28","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-19-1390"},{"key":"2026092210251333000_2026.09.14.751472v1.29","doi-asserted-by":"crossref","unstructured":"Lee, J.-S. et al. The insulin and IGF signaling pathway sustains breast cancer stem cells by IRS2\/PI3K-mediated regulation of MYC. Cell Rep. 41, (2022).","DOI":"10.1016\/j.celrep.2022.111759"},{"key":"2026092210251333000_2026.09.14.751472v1.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.humpath.2019.09.010"},{"key":"2026092210251333000_2026.09.14.751472v1.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-025-02857-2"},{"key":"2026092210251333000_2026.09.14.751472v1.32","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.10.024"},{"key":"2026092210251333000_2026.09.14.751472v1.33","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2010.12.014"},{"key":"2026092210251333000_2026.09.14.751472v1.34","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.2560-15.2015"},{"key":"2026092210251333000_2026.09.14.751472v1.35","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M708154200"},{"key":"2026092210251333000_2026.09.14.751472v1.36","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2023.07.036"},{"key":"2026092210251333000_2026.09.14.751472v1.37","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.05.012"},{"key":"2026092210251333000_2026.09.14.751472v1.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2016.04.002"},{"key":"2026092210251333000_2026.09.14.751472v1.39","doi-asserted-by":"publisher","DOI":"10.1242\/dev.00808"},{"key":"2026092210251333000_2026.09.14.751472v1.40","doi-asserted-by":"publisher","DOI":"10.1016\/S0896-6273(03)00163-6"},{"key":"2026092210251333000_2026.09.14.751472v1.41","doi-asserted-by":"publisher","DOI":"10.1038\/nature04684"},{"key":"2026092210251333000_2026.09.14.751472v1.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.ydbio.2010.05.012"},{"key":"2026092210251333000_2026.09.14.751472v1.43","unstructured":"Cmero, M. et al. Inferring structural variant cancer cell fraction. Nat. Commun. 11, 730 (2020)."},{"key":"2026092210251333000_2026.09.14.751472v1.44","doi-asserted-by":"crossref","unstructured":"Wong, J. M. et al. Abstract 630: Directly engaging participants in rare cancer research is feasible: the osteosarcoma and leiomyosarcoma projects. Cancer Res. 85, 630 (2025).","DOI":"10.1158\/1538-7445.AM2025-630"},{"key":"2026092210251333000_2026.09.14.751472v1.45","doi-asserted-by":"crossref","first-page":"11510","DOI":"10.1200\/JCO.2024.42.16_suppl.11510","article-title":"Prospective evaluation of pre-treatment ctDNA burden in localized osteosarcoma to identify patients with inferior outcomes: A report from the LEOPARD study","volume":"42","year":"2024","journal-title":"J. Clin. Oncol"},{"key":"2026092210251333000_2026.09.14.751472v1.46","doi-asserted-by":"crossref","unstructured":"Knudsen, E. S. et al. Pan-cancer molecular analysis of the RB tumor suppressor pathway. Commun. Biol. 3, 158 (2020).","DOI":"10.1038\/s42003-020-0873-9"},{"key":"2026092210251333000_2026.09.14.751472v1.47","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.17.9.5227"},{"key":"2026092210251333000_2026.09.14.751472v1.48","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.20.10.3633-3639.2000"},{"key":"2026092210251333000_2026.09.14.751472v1.49","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.19.7.4672"},{"key":"2026092210251333000_2026.09.14.751472v1.50","doi-asserted-by":"publisher","DOI":"10.64898\/2026.01.13.698472"},{"key":"2026092210251333000_2026.09.14.751472v1.51","doi-asserted-by":"crossref","first-page":"3259","DOI":"10.1158\/1078-0432.CCR-24-0563","article-title":"Mapping the Single-Cell Differentiation Landscape of Osteosarcoma","volume":"30","year":"2024","journal-title":"Clin. Cancer Res"},{"key":"2026092210251333000_2026.09.14.751472v1.52","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1038\/s43018-023-00595-y","article-title":"Cancer cell plasticity during tumor progression, metastasis and response to therapy","volume":"4","year":"2023","journal-title":"Nat. Cancer"},{"key":"2026092210251333000_2026.09.14.751472v1.53","doi-asserted-by":"publisher","DOI":"10.1016\/j.hoc.2025.04.002"},{"key":"2026092210251333000_2026.09.14.751472v1.54","doi-asserted-by":"publisher","DOI":"10.1158\/1535-7163.MCT-20-0987"},{"key":"2026092210251333000_2026.09.14.751472v1.55","doi-asserted-by":"crossref","first-page":"12695","DOI":"10.18632\/oncotarget.24268","article-title":"Detection of circulating tumor DNA in patients with osteosarcoma","volume":"9","year":"2018","journal-title":"Oncotarget"},{"key":"2026092210251333000_2026.09.14.751472v1.56","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"2026092210251333000_2026.09.14.751472v1.57","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2514"},{"key":"2026092210251333000_2026.09.14.751472v1.58","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-018-0051-x"},{"key":"2026092210251333000_2026.09.14.751472v1.59","doi-asserted-by":"crossref","unstructured":"Priebe, O. et al. Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations. Genome Biol. 27, 83 (2026).","DOI":"10.1186\/s13059-026-03971-w"},{"key":"2026092210251333000_2026.09.14.751472v1.60","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2203"},{"key":"2026092210251333000_2026.09.14.751472v1.61","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-45839-z"},{"key":"2026092210251333000_2026.09.14.751472v1.62","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.12.025"},{"key":"2026092210251333000_2026.09.14.751472v1.63","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0912402107"},{"key":"2026092210251333000_2026.09.14.751472v1.64","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx951"},{"key":"2026092210251333000_2026.09.14.751472v1.65","doi-asserted-by":"publisher","DOI":"10.1038\/nbt1010-1045"},{"key":"2026092210251333000_2026.09.14.751472v1.66","unstructured":"Smit, A. , Hubley, R. & Green, P. RepeatMasker Open-4.0. (2015)."},{"key":"2026092210251333000_2026.09.14.751472v1.67","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAF1250"},{"key":"2026092210251333000_2026.09.14.751472v1.68","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-018-5330-5"},{"key":"2026092210251333000_2026.09.14.751472v1.69","doi-asserted-by":"publisher","DOI":"10.1101\/2021.10.28.466333"},{"key":"2026092210251333000_2026.09.14.751472v1.70","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1015"},{"key":"2026092210251333000_2026.09.14.751472v1.71","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/s43018-020-0027-5","article-title":"A practical framework and online tool for mutational signature analyses show intertissue variation and driver dependencies","volume":"1","year":"2020","journal-title":"Nat. Cancer"},{"key":"2026092210251333000_2026.09.14.751472v1.72","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad719"},{"key":"2026092210251333000_2026.09.14.751472v1.73","unstructured":"Shimoyama, Y. pyCirclize: Circular visualization in Python. (2022)."},{"key":"2026092210251333000_2026.09.14.751472v1.74","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx346"},{"key":"2026092210251333000_2026.09.14.751472v1.75","doi-asserted-by":"crossref","unstructured":"Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).","DOI":"10.1038\/s41467-018-08200-y"},{"key":"2026092210251333000_2026.09.14.751472v1.76","doi-asserted-by":"publisher","DOI":"10.1101\/2024.05.06.592768"},{"key":"2026092210251333000_2026.09.14.751472v1.77","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1078"},{"key":"2026092210251333000_2026.09.14.751472v1.78","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"2026092210251333000_2026.09.14.751472v1.79","doi-asserted-by":"crossref","unstructured":"Taylor-Weiner, A. et al. Scaling computational genomics to millions of individuals with GPUs. Genome Biol. 20, 228 (2019).","DOI":"10.1186\/s13059-019-1836-7"},{"key":"2026092210251333000_2026.09.14.751472v1.80","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-1943-3"},{"key":"2026092210251333000_2026.09.14.751472v1.81","doi-asserted-by":"publisher","DOI":"10.1200\/CCI.21.00144"},{"key":"2026092210251333000_2026.09.14.751472v1.82","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-23-0467"},{"key":"2026092210251333000_2026.09.14.751472v1.83","doi-asserted-by":"publisher","DOI":"10.1200\/PO.17.00011"},{"key":"2026092210251333000_2026.09.14.751472v1.84","doi-asserted-by":"publisher","DOI":"10.1038\/nature12912"},{"key":"2026092210251333000_2026.09.14.751472v1.85","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-020-0905-x"},{"key":"2026092210251333000_2026.09.14.751472v1.86","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2026092210251333000_2026.09.14.751472v1.87","doi-asserted-by":"crossref","unstructured":"Li, B. & Dewey, C. N . RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).","DOI":"10.1186\/1471-2105-12-323"},{"key":"2026092210251333000_2026.09.14.751472v1.88","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad547"},{"key":"2026092210251333000_2026.09.14.751472v1.89","doi-asserted-by":"publisher","DOI":"10.1101\/2024.04.19.590243"},{"key":"2026092210251333000_2026.09.14.751472v1.90","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-025-02857-2"},{"key":"2026092210251333000_2026.09.14.751472v1.91","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.43803"},{"key":"2026092210251333000_2026.09.14.751472v1.92","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database Hallmark Gene Set Collection","volume":"1","year":"2015","journal-title":"Cell Syst"},{"key":"2026092210251333000_2026.09.14.751472v1.93","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4463"},{"key":"2026092210251333000_2026.09.14.751472v1.94","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.01.029"},{"key":"2026092210251333000_2026.09.14.751472v1.95","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00965-y"},{"key":"2026092210251333000_2026.09.14.751472v1.96","doi-asserted-by":"publisher","DOI":"10.64898\/2026.03.23.26349081"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.14.751472","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T17:25:25Z","timestamp":1790097925000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.14.751472"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,18]]},"references-count":96,"URL":"https:\/\/doi.org\/10.64898\/2026.09.14.751472","relation":{},"subject":[],"published":{"date-parts":[[2026,9,18]]},"subtype":"preprint"}}