AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
Here we present AmpliconSuite, a toolkit for focal amplification analysis from cancer whole-genome sequencing that identifies extrachromosomal DNA (ecDNA), breakage-fusion-bridges and other amplification modes. Its ecContext module categorizes ecDNA structures to understand formation mechanisms. Validation across 175 metaphase fluorescence in situ hybridization-probed genes in 72 models demonstrated accurate predictions. Analysis of 6,506 patient pan-cancer samples revealed ecDNA-mediated oncogene co-amplification preferences. To democratize data sharing, we created AmpliconRepository, a community-contributable platform, enabling investigation of results across >15,000 publicly hosted samples.
Authors
- Bhargavi Dameracharla (ORCID: https://orcid.org/0000-0001-5001-5057)
- Siavash R. Dehkordi (ORCID: https://orcid.org/0000-0003-3848-7267)
- Dhruv Khatri (ORCID: https://orcid.org/0000-0003-2139-9252)
- Gino Prasad (ORCID: https://orcid.org/0000-0003-4590-1278)
- Vineet Bafna (ORCID: https://orcid.org/0000-0002-5810-6241)
- Daniel Schreyer (ORCID: https://orcid.org/0000-0002-9788-0168)
- Thorin T. Tabor (ORCID: https://orcid.org/0000-0002-3369-1886)
- Aditi Gnanasekar (ORCID: https://orcid.org/0000-0002-8303-8674)
- Roel G.W. Verhaak (ORCID: https://orcid.org/0000-0003-2773-0436)
- Paul S. Mischel (ORCID: https://orcid.org/0000-0002-4560-2211)
- Ivy Tsz-Lo Wong (ORCID: https://orcid.org/0000-0002-9761-3422)
- Forrest Kim (ORCID: https://orcid.org/0000-0002-3141-4447)
- Viraj Deshpande (ORCID: https://orcid.org/0000-0002-4859-9409)
- Jens Luebeck (ORCID: https://orcid.org/0000-0003-4391-979X)
- Michael M. Reich (ORCID: https://orcid.org/0000-0003-4735-5514)
- Ted Liefeld (ORCID: https://orcid.org/0009-0002-0644-3630)
- Jill P. Mesirov (ORCID: https://orcid.org/0000-0002-9755-2818)
- Devika Torvi
- Michał Adamaszek (ORCID: https://orcid.org/0000-0003-3551-192X)
- Mădălina Giurgiu (ORCID: https://orcid.org/0000-0001-5007-7442)
- Rishaan Kenkre (ORCID: https://orcid.org/0000-0002-9029-9987)
- Kyra Fetter (ORCID: https://orcid.org/0009-0008-8306-8938)
- Tushar Agashe
- Hoon Kim (ORCID: https://orcid.org/0000-0003-4244-6126)
- Kaiyuan Zhu (ORCID: https://orcid.org/0000-0001-9976-6505)
- Rohil Ahuja (ORCID: https://orcid.org/0009-0005-1348-7852)
- Soyeon Kim (ORCID: https://orcid.org/0009-0004-6509-5490)
- Simone Spandau
- Peter Bailey
- Edwin Huang
- Michael Chan
Institutions
- Champalimaud Foundation (PT)
- Shanghai Jiao Tong University (CN)
- Discovery Institute (US)
- Yale University (US)
- University of California San Diego (US)
- Stanford Health Care (US)
- Mabvax Therapeutics (United States) (US)
- Stanford Medicine (US)
- Moores Cancer Center
- Charité - Universitätsmedizin Berlin (DE)
- University of Glasgow (GB)
- Sungkyunkwan University (KR)
- Stanford University (US)
Publication Details
- Journal
- Nature Methods
- Published
- 2026-10-16
- DOI
- https://doi.org/10.1038/s41592-026-03264-x
- Primary Topic
- Genomic variations and chromosomal abnormalities
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Brain Tumor Society
- Cancer Research UK
- Korea Health Industry Development Institute
- National Research Foundation of Korea
- Stiftung Würth
- Ministry of Science and ICT, South Korea
- National Institutes of Health
- Advanced Research Projects Agency
- National Cancer Institute