Evidence map›Paper›PMID 42888240›Full record

ArticleNature methods2026

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

Jens Luebeck, Ted Liefeld, Ivy Tsz-Lo Wong, Edwin Huang, Forrest Kim, Bhargavi Dameracharla, Michael Chan, Rohil Ahuja, Kyra Fetter, Dhruv Khatri and 21 more

Abstract read
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In one paragraph

Article in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

31 authors.

Jens Luebeck *Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. jluebeck@ucsd.edu.ORCID http://orcid.org/0000-0003-4391-979X
Ted Liefeld *Department of Medicine, University of California, San Diego, San Diego, CA, USA.ORCID http://orcid.org/0009-0002-0644-3630
Ivy Tsz-Lo Wong *Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Edwin Huang *Department of Medicine, University of California, San Diego, San Diego, CA, USA.
Forrest KimDepartment of Medicine, University of California, San Diego, San Diego, CA, USA.
Bhargavi DameracharlaDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Michael ChanDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.
Rohil AhujaDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.ORCID http://orcid.org/0009-0005-1348-7852
Kyra FetterDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.ORCID http://orcid.org/0009-0008-8306-8938
Dhruv KhatriDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.ORCID http://orcid.org/0009-0004-1597-9562
Kaiyuan ZhuDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-9976-6505
Thorin TaborDepartment of Medicine, University of California, San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0002-3369-1886
Daniel SchreyerSchool of Cancer Sciences, University of Glasgow, Scotland, UK.
Gino PrasadDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4590-1278
Aditi GnanasekarDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Siavash Raeisi DehkordiDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Simone SpandauDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Michał AdamaszekMOSEK ApS, Copenhagen, Denmark.
Rishaan KenkreDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.
Tushar AgasheDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.
Devika TorviDepartment of Bioengineering, University of California, San Diego, San Diego, CA, USA.
Mădălina Giurgiu-KraljičDepartment of Pediatric Oncology and Hematology, Charité - Universitätsmedizin Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0001-5007-7442
Soyeon KimDepartment of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea.ORCID http://orcid.org/0009-0004-6509-5490
Hoon KimDepartment of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea.ORCID http://orcid.org/0000-0003-4244-6126
Peter BaileyBotton-Champalimaud Pancreatic Cancer Center, Champalimaud Foundation, Lisbon, Portugal.
Roel G W VerhaakDepartment of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA.ORCID http://orcid.org/0000-0003-2773-0436
Viraj DeshpandeDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-4859-9409
Michael ReichDepartment of Medicine, University of California, San Diego, San Diego, CA, USA.ORCID http://orcid.org/0000-0003-4735-5514
Paul S MischelDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA. pmischel@stanford.edu.ORCID http://orcid.org/0000-0002-4560-2211
Jill P MesirovDepartment of Medicine, University of California, San Diego, San Diego, CA, USA. jmesirov@sbpdiscovery.org.ORCID http://orcid.org/0000-0002-9755-2818
Vineet BafnaDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. vbafna@ucsd.edu.ORCID http://orcid.org/0000-0002-5810-6241

Funding

eDyNAmiC - STANFORDOT2CA278688 · NCI · STANFORD UNIVERSITY · PI PAUL S MISCHEL · 2022 to 2026
$7.7M
eDyNAmiC - UCSDOT2CA278635 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2022 to 2026
$1.8M
eDyNAmiC - YALEOT2CA278649 · NCI · YALE UNIVERSITY · PI Roel GW Verhaak · 2022 to 2026
$1.6M
Platform and portal development for accessible, reproducible cancer genomics researchR50CA243876 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LIEFELD, JOHN THEODORE · 2019 to 2023
$1.1M
Cancer Research UK (CRUK) CGCATF-2021/100012Cancer Research UK (CRUK) CGCATF-2021/100016Cancer Research UK (CRUK) CGCATF-2021/100025Korea Health Industry Development Institute (KHIDI) HI19C1348National Research Foundation of Korea (NRF) NRF RS-2022-NR067592National Research Foundation of Korea (NRF) NRF RS-2023-NR077071U.S. Department of Health & Human Services | National Institutes of Health (NIH) NIH R01-CA238379U.S. Department of Health & Human Services | National Institutes of Health (NIH) R01-GM114362U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24-CA248457U.S. Department of Health & Human Services | National Institutes of Health (NIH) U24-CA258406U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) OT2CA278635U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) OT2CA278649U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) OT2CA278688U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) R50CA243876U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI) U24-CA264379
6 · The paper itself

Abstract

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.

Identifiers

PMID42888240

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.