{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T11:27:54Z","timestamp":1793532474099,"version":"4.5.0"},"reference-count":129,"publisher":"Springer Science and Business Media LLC","issue":"8037","license":[{"start":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2024,11,7]]},"DOI":"10.1038\/s41586-024-07955-3","type":"journal-article","created":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T16:02:04Z","timestamp":1728489724000},"page":"219-228","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":59,"title":["The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution"],"prefix":"10.1038","volume":"635","author":[{"given":"Duy D.","family":"Nguyen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William F.","family":"Hooper","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weisi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy R.","family":"Chu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather","family":"Geiger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer M.","family":"Shelton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minita","family":"Shah","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoe R.","family":"Goldstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lara","family":"Winterkorn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrienne","family":"Helland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0328-8359","authenticated-orcid":false,"given":"Michael","family":"Sigouros","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jyothi","family":"Manohar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4599-2969","authenticated-orcid":false,"given":"Jenna","family":"Moyer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Majd","family":"Al Assaad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alissa","family":"Semaan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8504-1690","authenticated-orcid":false,"given":"Florencia","family":"Madorsky Rowdo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Wilkes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohamed","family":"Osman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rahul R.","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6915-3070","authenticated-orcid":false,"given":"Andrea","family":"Sboner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henkel L.","family":"Valentine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Phillip","family":"Abbosh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2777-8587","authenticated-orcid":false,"given":"Scott T.","family":"Tagawa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David M.","family":"Nanus","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2302-4171","authenticated-orcid":false,"given":"Jones T.","family":"Nauseef","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3938-2627","authenticated-orcid":false,"given":"Cora N.","family":"Sternberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana M.","family":"Molina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Douglas","family":"Scherr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5566-0864","authenticated-orcid":false,"given":"Giorgio","family":"Inghirami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4666-6476","authenticated-orcid":false,"given":"Juan Miguel","family":"Mosquera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8061-9617","authenticated-orcid":false,"given":"Olivier","family":"Elemento","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5698-8183","authenticated-orcid":false,"given":"Nicolas","family":"Robine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6432-1693","authenticated-orcid":false,"given":"Bishoy M.","family":"Faltas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,10,9]]},"reference":[{"key":"7955_CR1","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.1038\/ng.3692","volume":"48","author":"BM Faltas","year":"2016","unstructured":"Faltas, B. M. et al. Clonal evolution of chemotherapy-resistant urothelial carcinoma. Nat. Genet. 48, 1490\u20131499 (2016).","journal-title":"Nat. Genet."},{"key":"7955_CR2","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.cell.2020.08.006","volume":"183","author":"K Hadi","year":"2020","unstructured":"Hadi, K. et al. Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs. Cell 183, 197\u2013210.e32 (2020).","journal-title":"Cell"},{"key":"7955_CR3","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1158\/2159-8290.CD-15-0344","volume":"5","author":"C Swanton","year":"2015","unstructured":"Swanton, C., McGranahan, N., Starrett, G. J. & Harris, R. S. APOBEC enzymes: mutagenic fuel for cancer evolution and heterogeneity. Cancer Discov. 5, 704\u2013712 (2015).","journal-title":"Cancer Discov."},{"key":"7955_CR4","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/s41586-020-1943-3","volume":"578","author":"LB Alexandrov","year":"2020","unstructured":"Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94\u2013101 (2020).","journal-title":"Nature"},{"key":"7955_CR5","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1038\/ng.2702","volume":"45","author":"SA Roberts","year":"2013","unstructured":"Roberts, S. A. et al. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat. Genet. 45, 970\u2013976 (2013).","journal-title":"Nat. Genet."},{"key":"7955_CR6","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1016\/j.cell.2012.04.024","volume":"149","author":"S Nik-Zainal","year":"2012","unstructured":"Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979\u2013993 (2012).","journal-title":"Cell"},{"key":"7955_CR7","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1158\/0008-5472.CAN-22-2912","volume":"83","author":"W Liu","year":"2023","unstructured":"Liu, W. et al. The cytidine deaminase APOBEC3G contributes to cancer mutagenesis and clonal evolution in bladder cancer. Cancer Res. 83, 506\u2013520 (2023).","journal-title":"Cancer Res."},{"key":"7955_CR8","doi-asserted-by":"publisher","first-page":"1732","DOI":"10.1038\/s41588-019-0525-5","volume":"51","author":"O Pich","year":"2019","unstructured":"Pich, O. et al. The mutational footprints of cancer therapies. Nat. Genet. 51, 1732\u20131740 (2019).","journal-title":"Nat. Genet."},{"key":"7955_CR9","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1016\/j.cell.2019.03.001","volume":"177","author":"JE Kucab","year":"2019","unstructured":"Kucab, J. E. et al. A compendium of mutational signatures of environmental agents. Cell 177, 821\u2013836.e16 (2019).","journal-title":"Cell"},{"key":"7955_CR10","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1126\/science.aba8347","volume":"370","author":"ARJ Lawson","year":"2020","unstructured":"Lawson, A. R. J. et al. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 370, 75\u201382 (2020).","journal-title":"Science"},{"key":"7955_CR11","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1126\/science.aba7300","volume":"370","author":"R Li","year":"2020","unstructured":"Li, R. et al. Macroscopic somatic clonal expansion in morphologically normal human urothelium. Science 370, 82\u201389 (2020).","journal-title":"Science"},{"key":"7955_CR12","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/s41586-019-1907-7","volume":"578","author":"M Gerstung","year":"2020","unstructured":"Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122\u2013128 (2020).","journal-title":"Nature"},{"key":"7955_CR13","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/s41586-020-2315-8","volume":"582","author":"AN Gorelick","year":"2020","unstructured":"Gorelick, A. N. et al. Phase and context shape the function of composite oncogenic mutations. Nature 582, 100\u2013103 (2020).","journal-title":"Nature"},{"key":"7955_CR14","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1016\/j.cell.2017.09.007","volume":"171","author":"AG Robertson","year":"2017","unstructured":"Robertson, A. G. et al. Comprehensive molecular characterization of muscle-invasive bladder cancer. Cell 171, 540\u2013556.e25 (2017).","journal-title":"Cell"},{"key":"7955_CR15","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1038\/s41586-019-1913-9","volume":"578","author":"Y Li","year":"2020","unstructured":"Li, Y. et al. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112\u2013121 (2020).","journal-title":"Nature"},{"key":"7955_CR16","doi-asserted-by":"publisher","first-page":"1911","DOI":"10.1042\/BST20221045","volume":"50","author":"LT Pecorino","year":"2022","unstructured":"Pecorino, L. T., Verhaak, R. G. W., Henssen, A. & Mischel, P. S. Extrachromosomal DNA (ecDNA): an origin of tumor heterogeneity, genomic remodeling, and drug resistance. Biochem. Soc. Trans. 50, 1911\u20131920 (2022).","journal-title":"Biochem. Soc. Trans."},{"key":"7955_CR17","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-08200-y","volume":"10","author":"V Deshpande","year":"2019","unstructured":"Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).","journal-title":"Nat. Commun."},{"key":"7955_CR18","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1038\/s41588-021-01000-z","volume":"54","author":"E van Leen","year":"2022","unstructured":"van Leen, E., Br\u00fcckner, L. & Henssen, A. G. The genomic and spatial mobility of extrachromosomal DNA and its implications for cancer therapy. Nat. Genet. 54, 107\u2013114 (2022).","journal-title":"Nat. Genet."},{"key":"7955_CR19","doi-asserted-by":"publisher","first-page":"1247","DOI":"10.1038\/s43018-022-00404-y","volume":"3","author":"L Bao","year":"2022","unstructured":"Bao, L., Zhong, X., Yang, Y. & Yang, L. Starfish infers signatures of complex genomic rearrangements across human cancers. Nat. Cancer 3, 1247\u20131259 (2022).","journal-title":"Nat. Cancer"},{"key":"7955_CR20","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/s41586-022-04398-6","volume":"602","author":"EN Bergstrom","year":"2022","unstructured":"Bergstrom, E. N. et al. Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. Nature 602, 510\u2013517 (2022).","journal-title":"Nature"},{"key":"7955_CR21","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1038\/s41586-020-1969-6","volume":"578","author":"The ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.","year":"2020","unstructured":"The ICGC\/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82\u201393 (2020).","journal-title":"Nature"},{"key":"7955_CR22","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1038\/s41588-020-0678-2","volume":"52","author":"H Kim","year":"2020","unstructured":"Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891\u2013897 (2020).","journal-title":"Nat. Genet."},{"key":"7955_CR23","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1038\/nrm3629","volume":"14","author":"C Bertoli","year":"2013","unstructured":"Bertoli, C., Skotheim, J. M. & de Bruin, R. A. M. Control of cell cycle transcription during G1 and S phases. Nat. Rev. Mol. Cell Biol. 14, 518\u2013528 (2013).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"7955_CR24","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1038\/s41588-022-01177-x","volume":"54","author":"JT Lange","year":"2022","unstructured":"Lange, J. T. et al. The evolutionary dynamics of extrachromosomal DNA in human cancers. Nat. Genet. 54, 1527\u20131533 (2022).","journal-title":"Nat. Genet."},{"key":"7955_CR25","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1158\/2159-8290.CD-22-0787","volume":"13","author":"P Dharanipragada","year":"2023","unstructured":"Dharanipragada, P. et al. Blocking genomic instability prevents acquired resistance to MAPK inhibitor therapy in melanoma. Cancer Discov. 13, 880\u2013909 (2023).","journal-title":"Cancer Discov."},{"key":"7955_CR26","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1016\/j.ccell.2021.03.006","volume":"39","author":"Y Zhu","year":"2021","unstructured":"Zhu, Y. et al. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 39, 694\u2013707.e7 (2021).","journal-title":"Cancer Cell"},{"key":"7955_CR27","doi-asserted-by":"publisher","first-page":"2239","DOI":"10.1016\/j.cell.2021.03.009","volume":"184","author":"SC Dentro","year":"2021","unstructured":"Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239\u20132254.e39 (2021).","journal-title":"Cell"},{"key":"7955_CR28","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-11291-0","volume":"7","author":"MBH Thomsen","year":"2017","unstructured":"Thomsen, M. B. H. et al. Comprehensive multiregional analysis of molecular heterogeneity in bladder cancer. Sci. Rep. 7, 11702 (2017).","journal-title":"Sci. Rep."},{"key":"7955_CR29","doi-asserted-by":"publisher","first-page":"2109","DOI":"10.1056\/NEJMoa1616288","volume":"376","author":"M Jamal-Hanjani","year":"2017","unstructured":"Jamal-Hanjani, M. et al. Tracking the evolution of non\u2013small-cell lung cancer. N. Engl. J. Med. 376, 2109\u20132121 (2017).","journal-title":"N. Engl. J. Med."},{"key":"7955_CR30","doi-asserted-by":"publisher","first-page":"816706","DOI":"10.3389\/fonc.2022.816706","volume":"12","author":"D Natesan","year":"2022","unstructured":"Natesan, D. et al. APOBEC mutational signature and tumor mutational burden as predictors of clinical outcomes and treatment response in patients with advanced urothelial cancer. Front. Oncol. 12, 816706 (2022).","journal-title":"Front. Oncol."},{"key":"7955_CR31","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1080\/15384101.2016.1152426","volume":"15","author":"AM Green","year":"2016","unstructured":"Green, A. M. et al. APOBEC3A damages the cellular genome during DNA replication. Cell Cycle 15, 998\u20131008 (2016).","journal-title":"Cell Cycle"},{"key":"7955_CR32","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1016\/j.cell.2019.02.012","volume":"176","author":"M Petljak","year":"2019","unstructured":"Petljak, M. et al. Characterizing mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis. Cell 176, 1282\u20131294.e20 (2019).","journal-title":"Cell"},{"key":"7955_CR33","doi-asserted-by":"publisher","unstructured":"Jones, R. T. et al. NPEPPS is a druggable driver of platinum resistance. Cancer Res. https:\/\/doi.org\/10.1158\/0008-5472.CAN-23-1976 (2024).","DOI":"10.1158\/0008-5472.CAN-23-1976"},{"key":"7955_CR34","doi-asserted-by":"publisher","first-page":"3823","DOI":"10.18632\/oncotarget.1709","volume":"5","author":"Y-W Chang","year":"2014","unstructured":"Chang, Y.-W. et al. Novel peptides suppress VEGFR-3 activity and antagonize VEGFR-3-mediated oncogenic effects. Oncotarget 5, 3823\u20133835 (2014).","journal-title":"Oncotarget"},{"key":"7955_CR35","doi-asserted-by":"publisher","first-page":"5140","DOI":"10.1002\/cncr.27496","volume":"118","author":"Y Hua","year":"2012","unstructured":"Hua, Y. et al. Slow down to stay alive: HER4 protects against cellular stress and confers chemoresistance in neuroblastoma. Cancer 118, 5140\u20135154 (2012).","journal-title":"Cancer"},{"key":"7955_CR36","doi-asserted-by":"publisher","first-page":"188","DOI":"10.3390\/biomedicines9020188","volume":"9","author":"B Bauvois","year":"2021","unstructured":"Bauvois, B. et al. Activation of interferon signaling in chronic lymphocytic leukemia cells contributes to apoptosis resistance via a JAK-Src\/STAT3\/Mcl-1 signaling pathway. Biomedicines 9, 188 (2021).","journal-title":"Biomedicines"},{"key":"7955_CR37","doi-asserted-by":"publisher","first-page":"3255","DOI":"10.7150\/ijbs.63125","volume":"17","author":"W Lin","year":"2021","unstructured":"Lin, W. et al. Discovery and validation of nitroxoline as a novel STAT3 inhibitor in drug-resistant urothelial bladder cancer. Int. J. Biol. Sci. 17, 3255\u20133267 (2021).","journal-title":"Int. J. Biol. Sci."},{"key":"7955_CR38","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1158\/1078-0432.CCR-13-1131","volume":"20","author":"M Juliachs","year":"2014","unstructured":"Juliachs, M. et al. The PDGFR\u03b2\u2013AKT pathway contributes to CDDP-acquired resistance in testicular germ cell tumors. Clin. Cancer Res. 20, 658\u2013667 (2014).","journal-title":"Clin. Cancer Res."},{"key":"7955_CR39","doi-asserted-by":"publisher","first-page":"8873","DOI":"10.3390\/molecules27248873","volume":"27","author":"Y Ji","year":"2022","unstructured":"Ji, Y. et al. Anlotinib exerts inhibitory effects against cisplatin-resistant ovarian cancer in vitro and in vivo. Molecules 27, 8873 (2022).","journal-title":"Molecules"},{"key":"7955_CR40","doi-asserted-by":"publisher","first-page":"1147","DOI":"10.1126\/science.aag0822","volume":"353","author":"M Baym","year":"2016","unstructured":"Baym, M. et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science 353, 1147\u20131151 (2016).","journal-title":"Science"},{"key":"7955_CR41","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/nature21356","volume":"543","author":"KM Turner","year":"2017","unstructured":"Turner, K. M. et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 543, 122\u2013125 (2017).","journal-title":"Nature"},{"key":"7955_CR42","doi-asserted-by":"publisher","DOI":"10.1186\/s12967-021-02927-x","volume":"19","author":"T Wang","year":"2021","unstructured":"Wang, T., Zhang, H., Zhou, Y. & Shi, J. Extrachromosomal circular DNA: a new potential role in cancer progression. J. Transl. Med. 19, 257 (2021).","journal-title":"J. Transl. Med."},{"key":"7955_CR43","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1007\/s00412-022-00773-4","volume":"131","author":"M Ili\u0107","year":"2022","unstructured":"Ili\u0107, M., Zaalberg, I. C., Raaijmakers, J. A. & Medema, R. H. Life of double minutes: generation, maintenance, and elimination. Chromosoma 131, 107\u2013125 (2022).","journal-title":"Chromosoma"},{"key":"7955_CR44","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1200\/JCO.23.02005","volume":"42","author":"F Meric-Bernstam","year":"2024","unstructured":"Meric-Bernstam, F. et al. Efficacy and safety of trastuzumab deruxtecan in patients with HER2-expressing solid tumors: primary results from the DESTINY-PanTumor02 phase II trial. J. Clin. Oncol. 42, 47\u201358 (2024).","journal-title":"J. Clin. Oncol."},{"key":"7955_CR45","doi-asserted-by":"publisher","first-page":"941","DOI":"10.1038\/s41388-023-02640-7","volume":"42","author":"Y Chen","year":"2023","unstructured":"Chen, Y., Qiu, Q., She, J. & Yu, J. Extrachromosomal circular DNA in colorectal cancer: biogenesis, function and potential as therapeutic target. Oncogene 42, 941\u2013951 (2023).","journal-title":"Oncogene"},{"key":"7955_CR46","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1016\/j.tig.2022.02.007","volume":"38","author":"JB Noer","year":"2022","unstructured":"Noer, J. B., H\u00f8rsdal, O. K., Xiang, X., Luo, Y. & Regenberg, B. Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends Genet. 38, 766\u2013781 (2022).","journal-title":"Trends Genet."},{"key":"7955_CR47","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/s41586-020-03064-z","volume":"591","author":"O Shoshani","year":"2021","unstructured":"Shoshani, O. et al. Chromothripsis drives the evolution of gene amplification in cancer. Nature 591, 137\u2013141 (2021).","journal-title":"Nature"},{"key":"7955_CR48","doi-asserted-by":"publisher","first-page":"884","DOI":"10.1038\/s41588-020-0667-5","volume":"52","author":"J Maciejowski","year":"2020","unstructured":"Maciejowski, J. et al. APOBEC3-dependent kataegis and TREX1-driven chromothripsis during telomere crisis. Nat. Genet. 52, 884\u2013890 (2020).","journal-title":"Nat. Genet."},{"key":"7955_CR49","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1016\/j.cell.2015.11.054","volume":"163","author":"J Maciejowski","year":"2015","unstructured":"Maciejowski, J., Li, Y., Bosco, N., Campbell, P. J. & de Lange, T. Chromothripsis and kataegis induced by telomere crisis. Cell 163, 1641\u20131654 (2015).","journal-title":"Cell"},{"key":"7955_CR50","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-45972-y","volume":"15","author":"JP Chen","year":"2024","unstructured":"Chen, J. P. et al. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat. Commun. 15, 1768 (2024).","journal-title":"Nat. Commun."},{"key":"7955_CR51","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1016\/j.cell.2021.01.002","volume":"184","author":"K Litchfield","year":"2021","unstructured":"Litchfield, K. et al. Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition. Cell 184, 596\u2013614.e14 (2021).","journal-title":"Cell"},{"key":"7955_CR52","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1002\/path.4886","volume":"242","author":"G Sj\u00f6dahl","year":"2017","unstructured":"Sj\u00f6dahl, G., Eriksson, P., Liedberg, F. & H\u00f6glund, M. Molecular classification of urothelial carcinoma: global mRNA classification versus tumour-cell phenotype classification. J. Pathol. 242, 113\u2013125 (2017).","journal-title":"J. Pathol."},{"key":"7955_CR53","doi-asserted-by":"publisher","first-page":"4289","DOI":"10.1158\/0008-5472.CAN-11-3549","volume":"72","author":"S Jirawatnotai","year":"2012","unstructured":"Jirawatnotai, S., Hu, Y., Livingston, D. M. & Sicinski, P. Proteomic identification of a direct role for cyclin D1 in DNA damage repair. Cancer Res. 72, 4289\u20134293 (2012).","journal-title":"Cancer Res."},{"key":"7955_CR54","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1038\/modpathol.2013.125","volume":"27","author":"R Seiler","year":"2014","unstructured":"Seiler, R., Thalmann, G. N., Rotzer, D., Perren, A. & Fleischmann, A. CCND1\/cyclinD1 status in metastasizing bladder cancer: a prognosticator and predictor of chemotherapeutic response. Mod. Pathol. 27, 87\u201395 (2014).","journal-title":"Mod. Pathol."},{"key":"7955_CR55","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-55636-3","volume":"9","author":"K Arora","year":"2019","unstructured":"Arora, K. et al. Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms. Sci. Rep. 9, 19123 (2019).","journal-title":"Sci. Rep."},{"key":"7955_CR56","doi-asserted-by":"publisher","unstructured":"Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https:\/\/doi.org\/10.48550\/arXiv.1303.3997 (2013).","DOI":"10.48550\/arXiv.1303.3997"},{"key":"7955_CR57","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","volume":"20","author":"A McKenna","year":"2010","unstructured":"McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297\u20131303 (2010).","journal-title":"Genome Res."},{"key":"7955_CR58","doi-asserted-by":"publisher","unstructured":"Benjamin, D. et al. Calling somatic SNVs and Indels with Mutect2. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/861054 (2019).","DOI":"10.1101\/861054"},{"key":"7955_CR59","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41592-018-0051-x","volume":"15","author":"S Kim","year":"2018","unstructured":"Kim, S. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods 15, 591\u2013594 (2018).","journal-title":"Nat. Methods"},{"key":"7955_CR60","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/s42003-018-0023-9","volume":"1","author":"G Narzisi","year":"2018","unstructured":"Narzisi, G. et al. Genome-wide somatic variant calling using localized colored de Bruijn graphs. Commun. Biol. 1, 20 (2018).","journal-title":"Commun. Biol."},{"key":"7955_CR61","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1101\/gr.221028.117","volume":"28","author":"JA Wala","year":"2018","unstructured":"Wala, J. A. et al. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 28, 581\u2013591 (2018).","journal-title":"Genome Res."},{"key":"7955_CR62","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1093\/bioinformatics\/btv710","volume":"32","author":"X Chen","year":"2016","unstructured":"Chen, X. et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32, 1220\u20131222 (2016).","journal-title":"Bioinformatics"},{"key":"7955_CR63","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2014-15-6-r84","volume":"15","author":"RM Layer","year":"2014","unstructured":"Layer, R. M., Chiang, C., Quinlan, A. R. & Hall, I. M. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).","journal-title":"Genome Biol."},{"key":"7955_CR64","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1093\/bioinformatics\/bts019","volume":"28","author":"A-K Emde","year":"2012","unstructured":"Emde, A.-K. et al. Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics 28, 619\u2013627 (2012).","journal-title":"Bioinformatics"},{"key":"7955_CR65","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1093\/nar\/30.1.38","volume":"30","author":"T Hubbard","year":"2002","unstructured":"Hubbard, T. The Ensembl genome database project. Nucleic Acids Res. 30, 38\u201341 (2002).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR66","doi-asserted-by":"publisher","first-page":"D941","DOI":"10.1093\/nar\/gky1015","volume":"47","author":"JG Tate","year":"2019","unstructured":"Tate, J. G. et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 47, D941\u2013D947 (2019).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR67","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nature15393","volume":"526","author":"The 1000 Genomes Project Consortium.","year":"2015","unstructured":"The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68\u201374 (2015).","journal-title":"Nature"},{"key":"7955_CR68","doi-asserted-by":"publisher","first-page":"D1062","DOI":"10.1093\/nar\/gkx1153","volume":"46","author":"MJ Landrum","year":"2018","unstructured":"Landrum, M. J. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46, D1062\u2013D1067 (2018).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR69","doi-asserted-by":"publisher","unstructured":"Adzhubei, I., Jordan, D. M. & Sunyaev, S. R. Predicting functional effect of human missense mutations using PolyPhen\u20102. Curr. Protoc. Hum. Genet. https:\/\/doi.org\/10.1002\/0471142905.hg0720s76 (2013).","DOI":"10.1002\/0471142905.hg0720s76"},{"key":"7955_CR70","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/nprot.2015.123","volume":"11","author":"R Vaser","year":"2016","unstructured":"Vaser, R., Adusumalli, S., Leng, S. N., Sikic, M. & Ng, P. C. SIFT missense predictions for genomes. Nat. Protoc. 11, 1\u20139 (2016).","journal-title":"Nat. Protoc."},{"key":"7955_CR71","doi-asserted-by":"publisher","DOI":"10.1186\/1479-7364-8-11","volume":"8","author":"HA Shihab","year":"2014","unstructured":"Shihab, H. A. et al. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum. Genomics 8, 11 (2014).","journal-title":"Hum. Genomics"},{"key":"7955_CR72","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/nature19057","volume":"536","author":"Exome Aggregation Consortium.","year":"2016","unstructured":"Exome Aggregation Consortium. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285\u2013291 (2016).","journal-title":"Nature"},{"key":"7955_CR73","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1093\/nar\/29.1.308","volume":"29","author":"ST Sherry","year":"2001","unstructured":"Sherry, S. T. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308\u2013311 (2001).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR74","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0974-4","volume":"17","author":"W McLaren","year":"2016","unstructured":"McLaren, W. et al. The Ensembl variant effect predictor. Genome Biol. 17, 122 (2016).","journal-title":"Genome Biol."},{"key":"7955_CR75","doi-asserted-by":"publisher","first-page":"D986","DOI":"10.1093\/nar\/gkt958","volume":"42","author":"JR MacDonald","year":"2014","unstructured":"MacDonald, J. R., Ziman, R., Yuen, R. K. C., Feuk, L. & Scherer, S. W. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 42, D986\u2013D992 (2014).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR76","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1038\/s41586-020-2287-8","volume":"581","author":"RL Collins","year":"2020","unstructured":"Collins, R. L. et al. A structural variation reference for medical and population genetics. Nature 581, 444\u2013451 (2020).","journal-title":"Nature"},{"key":"7955_CR77","doi-asserted-by":"publisher","first-page":"15.9.1","DOI":"10.1002\/cpbi.17","volume":"56","author":"KM Raine","year":"2016","unstructured":"Raine, K. M. et al. ascatNgs: identifying somatically acquired copy\u2010number alterations from whole\u2010genome sequencing data. Curr. Protoc. Bioinformatics 56, 15.9.1\u201315.9.17 (2016).","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"7955_CR78","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1093\/annonc\/mdu479","volume":"26","author":"F Favero","year":"2015","unstructured":"Favero, F. et al. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann. Oncol. 26, 64\u201370 (2015).","journal-title":"Ann. Oncol."},{"key":"7955_CR79","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-016-0893-4","volume":"17","author":"R Rosenthal","year":"2016","unstructured":"Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S. & Swanton, C. deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 17, 31 (2016).","journal-title":"Genome Biol."},{"key":"7955_CR80","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms9866","volume":"6","author":"S Kasar","year":"2015","unstructured":"Kasar, S. et al. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat. Commun. 6, 8866 (2015).","journal-title":"Nat. Commun."},{"key":"7955_CR81","doi-asserted-by":"publisher","unstructured":"Jupe, S. Chromatin modifying enzymes. Reactome https:\/\/doi.org\/10.3180\/react_172633.1 (2014).","DOI":"10.3180\/react_172633.1"},{"key":"7955_CR82","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nrc2876","volume":"10","author":"P Chi","year":"2010","unstructured":"Chi, P., Allis, C. D. & Wang, G. G. Covalent histone modifications\u2014miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer 10, 457\u2013469 (2010).","journal-title":"Nat. Rev. Cancer"},{"key":"7955_CR83","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/ng.907","volume":"43","author":"Y Gui","year":"2011","unstructured":"Gui, Y. et al. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet. 43, 875\u2013878 (2011).","journal-title":"Nat. Genet."},{"key":"7955_CR84","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1016\/j.cell.2013.03.008","volume":"153","author":"H Shen","year":"2013","unstructured":"Shen, H. & Laird, P. W. Interplay between the cancer genome and epigenome. Cell 153, 38\u201355 (2013).","journal-title":"Cell"},{"key":"7955_CR85","first-page":"64","volume":"7","author":"C Shyr","year":"2014","unstructured":"Shyr, C. et al. FLAGS, frequently mutated genes in public exomes. BMC Med. Genomics 7, 64 (2014).","journal-title":"Genomics"},{"key":"7955_CR86","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1038\/nature13182","volume":"507","author":"The FANTOM Consortium and the RIKEN PMI and CLST (DGT).","year":"2014","unstructured":"The FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature 507, 462\u2013470 (2014).","journal-title":"Nature"},{"key":"7955_CR87","doi-asserted-by":"publisher","unstructured":"Dalby, M., Rennie, S. & Andersson, R. Fantom5 transcribed enhancers In hg38. Zenodo https:\/\/doi.org\/10.5281\/zenodo.556775 (2017).","DOI":"10.5281\/zenodo.556775"},{"key":"7955_CR88","doi-asserted-by":"publisher","first-page":"934","DOI":"10.1016\/j.cell.2013.09.053","volume":"155","author":"D Hnisz","year":"2013","unstructured":"Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934\u2013947 (2013).","journal-title":"Cell"},{"key":"7955_CR89","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-14-128","volume":"14","author":"EY Chen","year":"2013","unstructured":"Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).","journal-title":"BMC Bioinformatics"},{"key":"7955_CR90","doi-asserted-by":"publisher","first-page":"W90","DOI":"10.1093\/nar\/gkw377","volume":"44","author":"MV Kuleshov","year":"2016","unstructured":"Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90\u2013W97 (2016).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR91","doi-asserted-by":"publisher","first-page":"e90","DOI":"10.1002\/cpz1.90","volume":"1","author":"Z Xie","year":"2021","unstructured":"Xie, Z. et al. Gene Set Knowledge Discovery with Enrichr. Curr. Protoc. 1, e90 (2021).","journal-title":"Curr. Protoc."},{"key":"7955_CR92","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1038\/s41592-020-01013-2","volume":"18","author":"M Tarabichi","year":"2021","unstructured":"Tarabichi, M. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat. Methods 18, 144\u2013155 (2021).","journal-title":"Nat. Methods"},{"key":"7955_CR93","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-015-0647-8","volume":"16","author":"V Popic","year":"2015","unstructured":"Popic, V. et al. Fast and scalable inference of multi-sample cancer lineages. Genome Biol. 16, 91 (2015).","journal-title":"Genome Biol."},{"key":"7955_CR94","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1126\/science.aau3879","volume":"362","author":"I Martincorena","year":"2018","unstructured":"Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911\u2013917 (2018).","journal-title":"Science"},{"key":"7955_CR95","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.1016\/j.cell.2017.09.042","volume":"171","author":"I Martincorena","year":"2017","unstructured":"Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029\u20131041.e21 (2017).","journal-title":"Cell"},{"key":"7955_CR96","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1126\/science.aaa6806","volume":"348","author":"I Martincorena","year":"2015","unstructured":"Martincorena, I. et al. High burden and pervasive positive selection of somatic mutations in normal human skin. Science 348, 880\u2013886 (2015).","journal-title":"Science"},{"key":"7955_CR97","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1146\/annurev-cancerbio-061421-012447","volume":"7","author":"A Herms","year":"2023","unstructured":"Herms, A. & Jones, P. H. Somatic mutations in normal tissues: new perspectives on early carcinogenesis. Annu. Rev. Cancer Biol. 7, 189\u2013205 (2023).","journal-title":"Annu. Rev. Cancer Biol."},{"key":"7955_CR98","doi-asserted-by":"publisher","unstructured":"Deshpande, A., Walradt, T., Hu, Y., Koren, A. & Imielinski, M. Robust foreground detection in somatic copy number data. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/847681 (2019).","DOI":"10.1101\/847681"},{"key":"7955_CR99","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1016\/j.cell.2016.12.025","volume":"168","author":"M Imielinski","year":"2017","unstructured":"Imielinski, M., Guo, G. & Meyerson, M. Insertions and deletions target lineage-defining genes in human cancers. Cell 168, 460\u2013472.e14 (2017).","journal-title":"Cell"},{"key":"7955_CR100","doi-asserted-by":"publisher","first-page":"e161370","DOI":"10.1172\/jci.insight.161370","volume":"7","author":"M Zhou","year":"2022","unstructured":"Zhou, M. et al. Patterns of structural variation define prostate cancer across disease states. JCI Insight 7, e161370 (2022).","journal-title":"JCI Insight"},{"key":"7955_CR101","doi-asserted-by":"publisher","first-page":"D1115","DOI":"10.1093\/nar\/gkab959","volume":"50","author":"BT Lee","year":"2022","unstructured":"Lee, B. T. et al. The UCSC Genome Browser database: 2022 update. Nucleic Acids Res. 50, D1115\u2013D1122 (2022).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR102","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1038\/s41568-018-0060-1","volume":"18","author":"Z Sondka","year":"2018","unstructured":"Sondka, Z. et al. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat. Rev. Cancer 18, 696\u2013705 (2018).","journal-title":"Nat. Rev. Cancer"},{"key":"7955_CR103","doi-asserted-by":"publisher","first-page":"3470","DOI":"10.1093\/bioinformatics\/btac335","volume":"38","author":"EN Bergstrom","year":"2022","unstructured":"Bergstrom, E. N., Kundu, M., Tbeileh, N. & Alexandrov, L. B. Examining clustered somatic mutations with SigProfilerClusters. Bioinformatics 38, 3470\u20133473 (2022).","journal-title":"Bioinformatics"},{"key":"7955_CR104","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"7955_CR105","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1093\/bioinformatics\/btv642","volume":"32","author":"BA Veeneman","year":"2016","unstructured":"Veeneman, B. A., Shukla, S., Dhanasekaran, S. M., Chinnaiyan, A. M. & Nesvizhskii, A. I. Two-pass alignment improves novel splice junction quantification. Bioinformatics 32, 43\u201349 (2016).","journal-title":"Bioinformatics"},{"key":"7955_CR106","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923\u2013930 (2014).","journal-title":"Bioinformatics"},{"key":"7955_CR107","doi-asserted-by":"publisher","first-page":"lqaa078","DOI":"10.1093\/nargab\/lqaa078","volume":"2","author":"Y Zhang","year":"2020","unstructured":"Zhang, Y., Parmigiani, G. & Johnson, W. E. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom. Bioinform. 2, lqaa078 (2020).","journal-title":"NAR Genom. Bioinform."},{"key":"7955_CR108","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"7955_CR109","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1016\/j.cell.2018.03.022","volume":"173","author":"KA Hoadley","year":"2018","unstructured":"Hoadley, K. A. et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell 173, 291\u2013304.e6 (2018).","journal-title":"Cell"},{"key":"7955_CR110","doi-asserted-by":"publisher","first-page":"D56","DOI":"10.1093\/nar\/gks1172","volume":"41","author":"KR Rosenbloom","year":"2012","unstructured":"Rosenbloom, K. R. et al. ENCODE data in the UCSC Genome browser: year 5 update. Nucleic Acids Res. 41, D56\u2013D63 (2012).","journal-title":"Nucleic Acids Res."},{"key":"7955_CR111","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18099-z","volume":"11","author":"J Luebeck","year":"2020","unstructured":"Luebeck, J. et al. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat. Commun. 11, 4374 (2020).","journal-title":"Nat. Commun."},{"key":"7955_CR112","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).","journal-title":"Bioinformatics"},{"key":"7955_CR113","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"7955_CR114","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1038\/s41592-020-00971-x","volume":"17","author":"M Kolmogorov","year":"2020","unstructured":"Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103\u20131110 (2020).","journal-title":"Nat. Methods"},{"key":"7955_CR115","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.1038\/mt.2008.156","volume":"16","author":"MM Lufino","year":"2008","unstructured":"Lufino, M. M., Edser, P. A. & Wade-Martins, R. Advances in high-capacity extrachromosomal vector technology: episomal maintenance, vector delivery, and transgene expression. Mol. Ther. 16, 1525\u20131538 (2008).","journal-title":"Mol. Ther."},{"key":"7955_CR116","doi-asserted-by":"publisher","first-page":"702","DOI":"10.15252\/emmm.201505869","volume":"8","author":"C Jin","year":"2016","unstructured":"Jin, C. et al. Safe engineering of CAR T cells for adoptive cell therapy of cancer using long\u2010term episomal gene transfer. EMBO Mol. Med. 8, 702\u2013711 (2016).","journal-title":"EMBO Mol. Med."},{"key":"7955_CR117","doi-asserted-by":"publisher","first-page":"3913","DOI":"10.1158\/0008-5472.CAN-14-0247","volume":"74","author":"MD Hall","year":"2014","unstructured":"Hall, M. D. et al. Say no to DMSO: dimethylsulfoxide inactivates cisplatin, carboplatin, and other platinum complexes. Cancer Res. 74, 3913\u20133922 (2014).","journal-title":"Cancer Res."},{"key":"7955_CR118","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1382-0","volume":"19","author":"FA Wolf","year":"2018","unstructured":"Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).","journal-title":"Genome Biol."},{"key":"7955_CR119","doi-asserted-by":"publisher","unstructured":"Virshup, I., Rybakov, S., Theis, F. J., Angerer, P. & Wolf, F. A. anndata: annotated data. Preprint at bioRxiv https:\/\/doi.org\/10.1101\/2021.12.16.473007 (2021).","DOI":"10.1101\/2021.12.16.473007"},{"key":"7955_CR120","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","volume":"16","author":"I Korsunsky","year":"2019","unstructured":"Korsunsky, I. et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat. Methods 16, 1289\u20131296 (2019).","journal-title":"Nat. Methods"},{"key":"7955_CR121","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","volume":"1","author":"A Liberzon","year":"2015","unstructured":"Liberzon, A. et al. The Molecular Signatures Database Hallmark Gene Set Collection. Cell Syst. 1, 417\u2013425 (2015).","journal-title":"Cell Syst."},{"key":"7955_CR122","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1002\/cyto.990010114","volume":"1","author":"MH Fox","year":"1980","unstructured":"Fox, M. H. A model for the computer analysis of synchronous DNA distributions obtained by flow cytometry. Cytometry 1, 71\u201377 (1980).","journal-title":"Cytometry"},{"key":"7955_CR123","doi-asserted-by":"publisher","first-page":"a006227","DOI":"10.1101\/mcs.a006227","volume":"8","author":"J Cyrta","year":"2022","unstructured":"Cyrta, J. et al. Whole-genome characterization of myoepithelial carcinomas of the soft tissue. Cold Spring Harb. Mol. Case Stud. 8, a006227 (2022).","journal-title":"Cold Spring Harb. Mol. Case Stud."},{"key":"7955_CR124","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1593\/neo.121550","volume":"15","author":"JM Mosquera","year":"2013","unstructured":"Mosquera, J. M. et al. Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer. Neoplasia 15, 1\u201310 (2013).","journal-title":"Neoplasia"},{"key":"7955_CR125","doi-asserted-by":"publisher","first-page":"4579","DOI":"10.1158\/0008-5472.CAN-16-3394","volume":"77","author":"AM Green","year":"2017","unstructured":"Green, A. M. et al. Cytosine deaminase APOBEC3A sensitizes leukemia cells to inhibition of the DNA replication checkpoint. Cancer Res. 77, 4579\u20134588 (2017).","journal-title":"Cancer Res."},{"key":"7955_CR126","doi-asserted-by":"publisher","first-page":"13759","DOI":"10.1073\/pnas.0606179103","volume":"103","author":"K-J Shin","year":"2006","unstructured":"Shin, K.-J. et al. A single lentiviral vector platform for microRNA-based conditional RNA interference and coordinated transgene expression. Proc. Natl Acad. Sci. USA 103, 13759\u201313764 (2006).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"7955_CR127","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"7955_CR128","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1158\/1535-7163.MCT-14-0765","volume":"14","author":"AG Goglia","year":"2015","unstructured":"Goglia, A. G. et al. Identification of novel radiosensitizers in a high-throughput, cell-based screen for DSB repair inhibitors. Mol. Cancer Ther. 14, 326\u2013342 (2015).","journal-title":"Mol. Cancer Ther."},{"key":"7955_CR129","doi-asserted-by":"publisher","unstructured":"Nguyen, D. D. et al. The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution. Zenodo https:\/\/doi.org\/10.5281\/zenodo.11121869 (2024).","DOI":"10.5281\/zenodo.11121869"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07955-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07955-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07955-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,6]],"date-time":"2024-11-06T13:09:22Z","timestamp":1730898562000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41586-024-07955-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,9]]},"references-count":129,"journal-issue":{"issue":"8037","published-print":{"date-parts":[[2024,11,7]]}},"alternative-id":["7955"],"URL":"https:\/\/doi.org\/10.1038\/s41586-024-07955-3","relation":{},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,9]]},"assertion":[{"value":"28 April 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 August 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 October 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"B.M.F.: consulting or advisory role for QED therapeutics, Boston Gene, Astrin Biosciences Merck, Immunomedics\/Gilead, QED therapeutics, Guardant and Janssen; patent royalties from Immunomedics\/Gilead; research support from Eli Lilly; and honoraria from Urotoday. O.E.: stock and other ownership interests from Freenome, OneThree Biotech, Owkin\u00a0and Volastra Therapeutics, and personal fees from Pionyr Immunotherapeutics\u00a0and Champions Oncology. S.T.T.: consulting or advisory role for 4D Pharma, Abbvie, AIkido Pharma, Amgen, Astellas Pharma, Bayer, Blue Earth Diagnostics, Clarity Pharmaceuticals, Clovis Oncology, Convergent Therapeutics, Dendreon, Endocyte, Genentech, Genomic Health, Gilead Sciences, Immunomedics, Janssen, Karyopharm Therapeutics, Medivation, Myovant Sciences, Novartis, Pfizer, POINT Biopharma, QED Therapeutics, Sanofi, Seagen, Telix Pharmaceuticals\u00a0and Tolmar; research funding from Abbvie, Amgen, Astellas Pharma, AstraZeneca, AVEO, Bayer, Boehringer Ingelheim, Bristol-Myers Squibb, Clovis Oncology, Dendreon, Endocyte, Exelixis, Genentech, Immunomedics, Inovio Pharmaceuticals, Janssen, Karyopharm Therapeutics, Lilly, Medivation, Merck, Millennium, Newlink Genetics, Novartis, POINT Biopharma, Progenics, Rexahn Pharmaceuticals, Sanofi\u00a0and Stem CentRx; patents, royalties, other intellectual property or patent royalty from Immunomedics\/Gilead; travel, accommodation and expenses from Amgen, Immunomedics\u00a0and Sanofi; and uncompensated relationships from ATLAB Pharma\u00a0and Phosplatin Therapeutics. D.M.N.: consulting or advisory role for AstraZeneca,\u00a0and\u00a0research funding from AstraZeneca, Boehringer Ingelheim, Clovis Oncology, Exelixis, Immumedics, Janssen, Novartis, Pfizer\u00a0and Zenith Epigenetics. J.T.N.: consulting or advisory role for AIQ Solutions, and travel, accommodation or expenses from Digital Science Press. C.N.S.: consulting or advisory role for Astellas Pharma, AstraZeneca, Bayer, Bristol-Myers Squibb\/Medarex, Foundation Medicine, Genzyme, Immunomedics, IMPAC Medical Systems, Incyte, Medscape, Merck, MSD, Pfizer, Roche\u00a0and UroToday. A.M.M.: consulting or advisory role for Eisai, Exelixis\u00a0and Janssen. J.M.M.: research funding from Personal Genome Diagnostics, and travel, accommodation or expenses from Personal Genome Diagnostics. D.S.: research funding from Urogen Pharma, Cepheid, Anchiano\u00a0and CryoLife. P.A.: stock and other ownership interests with Abyost Pharmaceuticals; consulting or advisory role for ArTara Therapeutics; research funding from Adaptive Biotechnologies, Janssen Oncology\u00a0and natera; and\u00a0patents, royalties or other intellectual property from intravesical imidazolium compounds and\u00a0urine biomarkers patent application. D.D.N., W.F.H., T.R.C., H.G., J.M.S., M.\u2009Shah, Z.R.G., L.W., A.H., M.\u2009Sigouros, J.\u2009Manohar, J.\u2009Moyer, M.A.A., A.\u2009Semaan, S.C., F.M.R., D.W., M.O., R.R.S., W.L., H.L.V., A.\u2009Sboner, G.I. and N.R. declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}