{ "abstract": "Focal amplifications in the cancer genome, particularly extrachromosomal DNA (ecDNA) amplifications, are emerging as a pivotal event in cancer progression across diverse cancer contexts, presenting a paradigm shift in our understanding of tumor dynamics. Simultaneously, identification of the various modes of focal amplifications is bioinformatically challenging. We present AmpliconSuite, a collection of tools that enables robust identification of focal amplifications from whole-genome sequencing data. AmpliconSuite includes AmpliconSuite- pipeline; utilizing the AmpliconArchitect (AA) method, and AmpliconRepository.org; a community- editable website for the sharing of focal amplification calls. We also describe improvements made to AA since its initial release that improve its accuracy and speed. As a proof of principle, we utilized publicly available pan-cancer datasets encompassing 2,525 tumor samples hosted on AmpliconRepository.org to illustrate important properties of focal amplifications, showing ecDNA has higher copy number, and stronger oncogene enrichment, compared to other classes of focal amplifications. Finally, we illustrate how AmpliconSuite-pipeline enables delineation of the various mechanisms by which ecDNA forms.", "abstract_shown": true, "affiliations": [ "Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. jluebeck@ucsd.edu", "Department of Medicine, University of California, San Diego, San Diego, CA, USA", "Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA", "Sarafan Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA", "Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA", "Department of Bioengineering, University of California, San Diego, San Diego, CA, USA", "School of Computer Science, Shanghai Jiao Tong University, Shanghai, China", "School of Cancer Sciences, University of Glasgow, Scotland, UK", "MOSEK ApS, Copenhagen, Denmark", "Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany", "Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea", "Botton-Champalimaud Pancreatic Cancer Center, Champalimaud Foundation, Lisbon, Portugal", "Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA", "Mivax Therapeutics Inc., San Francisco, CA, USA", "The Bioinformatics Shop LLC, San Francisco, CA, USA", "Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. pmischel@stanford.edu", "Sarafan Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA. pmischel@stanford.edu", "Department of Medicine, University of California, San Diego, San Diego, CA, USA. jmesirov@sbpdiscovery.org", "Moores Cancer Center, University of California, San Diego, San Diego, CA, USA. jmesirov@sbpdiscovery.org", "Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA. jmesirov@sbpdiscovery.org", "Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. vbafna@ucsd.edu", "Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA. vbafna@ucsd.edu", "Moores Cancer Center, University of California, San Diego, San Diego, CA, USA. vbafna@ucsd.edu" ], "article_type": null, "arxiv": null, "author_total": 31, "authors": [ { "affs": [ 0 ], "name": "Jens Luebeck", "orcid": "0000-0003-4391-979X" }, { "affs": [ 1 ], "name": "Ted Liefeld", "orcid": "0009-0002-0644-3630" }, { "affs": [ 2, 3 ], "name": "Ivy Tsz-Lo Wong", "orcid": "0000-0002-9761-3422" }, { "affs": [ 1 ], "name": "Edwin Huang" }, { "affs": [ 1 ], "name": "Forrest Kim", "orcid": "0000-0002-3141-4447" }, { "affs": [ 4 ], "name": "Bhargavi Dameracharla", "orcid": "0000-0001-5001-5057" }, { "affs": [ 5 ], "name": "Michael Chan" }, { "affs": [ 5 ], "name": "Rohil Ahuja", "orcid": "0009-0005-1348-7852" }, { "affs": [ 5 ], "name": "Kyra Fetter", "orcid": "0009-0008-8306-8938" }, { "affs": [ 5 ], "name": "Dhruv Khatri", "orcid": "0000-0003-2139-9252" }, { "affs": [ 4, 6 ], "name": "Kaiyuan Zhu", "orcid": "0000-0001-9976-6505" }, { "affs": [ 1 ], "name": "Thorin T. Tabor", "orcid": "0000-0002-3369-1886" }, { "affs": [ 7 ], "name": "Daniel Schreyer", "orcid": "0000-0002-9788-0168" }, { "affs": [ 4 ], "name": "Gino Prasad", "orcid": "0000-0003-4590-1278" }, { "affs": [ 2, 3 ], "name": "Aditi Gnanasekar", "orcid": "0000-0002-8303-8674" }, { "affs": [ 4 ], "name": "Siavash R. Dehkordi", "orcid": "0000-0003-3848-7267" }, { "affs": [ 4 ], "name": "Simone Spandau" }, { "affs": [ 8 ], "name": "Michał Adamaszek", "orcid": "0000-0003-3551-192X" }, { "affs": [ 5 ], "name": "Rishaan Kenkre", "orcid": "0000-0002-9029-9987" }, { "affs": [ 5 ], "name": "Tushar Agashe" }, { "affs": [ 5 ], "name": "Devika Torvi" }, { "affs": [ 9 ], "name": "Mădălina Giurgiu", "orcid": "0000-0001-5007-7442" }, { "affs": [ 10 ], "name": "Soyeon Kim", "orcid": "0009-0004-6509-5490" }, { "affs": [ 10 ], "name": "Hoon Kim", "orcid": "0000-0003-4244-6126" }, { "affs": [ 11 ], "name": "Peter Bailey" }, { "affs": [ 12 ], "name": "Roel G.W. Verhaak", "orcid": "0000-0003-2773-0436" }, { "affs": [ 4, 13, 14 ], "name": "Viraj Deshpande", "orcid": "0000-0002-4859-9409" }, { "affs": [ 1 ], "name": "Michael M. Reich", "orcid": "0000-0003-4735-5514" }, { "affs": [ 15, 16 ], "name": "Paul S. Mischel", "orcid": "0000-0002-4560-2211" }, { "affs": [ 17, 18, 19 ], "name": "Jill P. Mesirov", "orcid": "0000-0002-9755-2818" }, { "affs": [ 20, 21, 22 ], "name": "Vineet Bafna", "orcid": "0000-0002-5810-6241" } ], "bibtex": "https://research.draconitic.com/paper/f83qzfc9cn3cp.bib", "cited_by": 30, "doi": "10.1038/s41592-026-03264-x", "fulltext_url": null, "id": "f83qzfc9cn3cp", "issns": [ "1548-7091", "1548-7105" ], "landing_url": "https://doi.org/10.1038/s41592-026-03264-x", "language": "en", "licence": "CC-BY", "licence_label": "CC BY", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1311|Genomic variations and chromosomal abnormalities" ] ], "openalex": "W7222401541", "pdf_url": "https://www.nature.com/articles/s41592-026-03264-x.pdf", "pmcid": null, "pmid": "42888240", "published": "2026-10-16", "publisher": "Nature Portfolio", "ris": "https://research.draconitic.com/paper/f83qzfc9cn3cp.ris", "sources": [ { "first_seen": "2026-11-04T13:21:05Z", "native_id": "W7222401541", "source": "openalex", "url": "https://doi.org/10.1038/s41592-026-03264-x" } ], "subjects": [ { "field": "biology", "origin": "openalex:1311|Genomic variations and chromosomal abnormalities", "subfield": "genetics-genomics" } ], "title": "AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes", "title_text": "AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes", "type": "peer-reviewed", "updated_at": "2026-11-08T13:20:41Z", "url": "https://research.draconitic.com/paper/f83qzfc9cn3cp", "venue": "Nature Methods", "versions": [] }