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Peer-reviewedCC BYNature Methods

AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes

  • Jens Luebeck1
  • Ted Liefeld2
  • Ivy Tsz-Lo Wong3,4
  • Edwin Huang2
  • Forrest Kim2
  • Bhargavi Dameracharla5
  • Michael Chan6
  • Rohil Ahuja6
  • Kyra Fetter6
  • Dhruv Khatri6
  • Kaiyuan Zhu5,7
  • Thorin T. Tabor2
19 more authors
  • Daniel Schreyer8
  • Gino Prasad5
  • Aditi Gnanasekar3,4
  • Siavash R. Dehkordi5
  • Simone Spandau5
  • Michał Adamaszek9
  • Rishaan Kenkre6
  • Tushar Agashe6
  • Devika Torvi6
  • Mădălina Giurgiu10
  • Soyeon Kim11
  • Hoon Kim11
  • Peter Bailey12
  • Roel G.W. Verhaak13
  • Viraj Deshpande5,14,15
  • Michael M. Reich2
  • Paul S. Mischel16,17
  • Jill P. Mesirov18,19,20
  • Vineet Bafna21,22,23
23 affiliations
  1. 1Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. [email protected]
  2. 2Department of Medicine, University of California, San Diego, San Diego, CA, USA
  3. 3Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
  4. 4Sarafan Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA
  5. 5Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
  6. 6Department of Bioengineering, University of California, San Diego, San Diego, CA, USA
  7. 7School of Computer Science, Shanghai Jiao Tong University, Shanghai, China
  8. 8School of Cancer Sciences, University of Glasgow, Scotland, UK
  9. 9MOSEK ApS, Copenhagen, Denmark
  10. 10Department of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany
  11. 11Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea
  12. 12Botton-Champalimaud Pancreatic Cancer Center, Champalimaud Foundation, Lisbon, Portugal
  13. 13Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
  14. 14Mivax Therapeutics Inc., San Francisco, CA, USA
  15. 15The Bioinformatics Shop LLC, San Francisco, CA, USA
  16. 16Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA. [email protected]
  17. 17Sarafan Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA. [email protected]
  18. 18Department of Medicine, University of California, San Diego, San Diego, CA, USA. [email protected]
  19. 19Moores Cancer Center, University of California, San Diego, San Diego, CA, USA. [email protected]
  20. 20Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA. [email protected]
  21. 21Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. [email protected]
  22. 22Halıcıoğlu Data Science Institute, University of California, San Diego, San Diego, CA, USA. [email protected]
  23. 23Moores Cancer Center, University of California, San Diego, San Diego, CA, USA. [email protected]
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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.

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Cite

BibTeXRIS
BibTeX
@article{luebeck2026ampliconsuite,
  title = {{AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes}},
  author = {Jens Luebeck and Ted Liefeld and Ivy Tsz-Lo Wong and Edwin Huang and Forrest Kim and Bhargavi Dameracharla and Michael Chan and Rohil Ahuja and Kyra Fetter and Dhruv Khatri and Kaiyuan Zhu and Thorin T. Tabor and Daniel Schreyer and Gino Prasad and Aditi Gnanasekar and Siavash R. Dehkordi and Simone Spandau and Michał Adamaszek and Rishaan Kenkre and Tushar Agashe and Devika Torvi and Mădălina Giurgiu and Soyeon Kim and Hoon Kim and Peter Bailey and Roel G.W. Verhaak and Viraj Deshpande and Michael M. Reich and Paul S. Mischel and Jill P. Mesirov and Vineet Bafna},
  journal = {Nature Methods},
  year = {2026},
  month = oct,
  doi = {10.1038/s41592-026-03264-x},
  url = {https://doi.org/10.1038/s41592-026-03264-x},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes
AU  - Jens Luebeck
AU  - Ted Liefeld
AU  - Ivy Tsz-Lo Wong
AU  - Edwin Huang
AU  - Forrest Kim
AU  - Bhargavi Dameracharla
AU  - Michael Chan
AU  - Rohil Ahuja
AU  - Kyra Fetter
AU  - Dhruv Khatri
AU  - Kaiyuan Zhu
AU  - Thorin T. Tabor
AU  - Daniel Schreyer
AU  - Gino Prasad
AU  - Aditi Gnanasekar
AU  - Siavash R. Dehkordi
AU  - Simone Spandau
AU  - Michał Adamaszek
AU  - Rishaan Kenkre
AU  - Tushar Agashe
AU  - Devika Torvi
AU  - Mădălina Giurgiu
AU  - Soyeon Kim
AU  - Hoon Kim
AU  - Peter Bailey
AU  - Roel G.W. Verhaak
AU  - Viraj Deshpande
AU  - Michael M. Reich
AU  - Paul S. Mischel
AU  - Jill P. Mesirov
AU  - Vineet Bafna
PY  - 2026
DA  - 2026/10/16
JO  - Nature Methods
DO  - 10.1038/s41592-026-03264-x
UR  - https://doi.org/10.1038/s41592-026-03264-x
AB  - 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.
SN  - 1548-7091
SN  - 1548-7105
ER  -