ArticleNature genetics2020
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.
Registry-linked trialAbstract read
In one paragraph
Article in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05827614 (An Open-Label, Multicenter, First-in-Human, Dose-Escalation and Dose-Expansion, Phase 1/2 Study of BBI-355 and BBI-355 in Combination With Select Targeted Therapies in Subjects With Locally Advanced or Metastatic Solid Tumors With Oncogene Amplifications), which is not on this map. Cited by 361 papers.
0numbers the graph read from it
0cells of the map it votes in
361citing papers in PubMed
–field-weighted citation impact
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.
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.
An Open-Label, Multicenter, First-in-Human, Dose-Escalation and Dose-Expansion, Phase 1/2 Study of BBI-355 and BBI-355 in Combination With Select Targeted Therapies in Subjects With Locally Advanced or Metastatic Solid Tumors With Oncogene Amplifications
Who cites it
361 citing papers in PubMed.
- Phase 2 Study of Amivantamab Plus Lazertinib in Previously Treated Patients With EGFR-Mutant Lung Cancers With Brain and Leptomeningeal Metastases.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2026Trial
- AmpliconSuite: an end-to-end workflow for analyzing focal amplifications in cancer genomes.Nature methods · 2026Article
- Reframing cancer therapy through tumor plasticity.Nature cancer · 2026Review
- Micronuclear ecDNA constrains tumor cell fitness and is associated with favorable patient survival.Nature genetics · 2026Article
- Circulating tumour DNA and extrachromosomal DNA in prostate and bladder cancer: biology, clinical applications and future perspectives.World journal of urology · 2026Review
- Article
- Unraveling the lexicon of complex mutational phenomena in human cancers.Nature cancer · 2026Review
- Extrachromosomal DNA as a platform for epigenetic reprogramming in cancer.Molecular cancer · 2026Review
- The shared evolutionary capacities of plasmids and extrachromosomal DNA.Nature reviews. Genetics · 2026Review
- Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints.bioRxiv : the preprint server for biology · 2026Article
- Article
- Integrating molecular subtypes, genomics and functional dependencies to identify context-specific therapeutic vulnerabilities in small cell lung cancer.Biomarker research · 2026Review
- Extrachromosomal DNA in urothelial carcinoma: mechanisms and clinical applications.Nature reviews. Urology · 2026Review
- Advancing the applications of liquid biopsies in oncology.Nature reviews. Genetics · 2026Review
- Origins and consequences of oncogenic 3D chromatin remodelling.Nature reviews. Cancer · 2026Review
- Exploring the landscape of targetable alterations in patients with glioblastoma.Nature reviews. Clinical oncology · 2026Review
- scAmp enables focal gene amplification analysis from single-cell data.Nature communications · 2026Article
- Examining the role of extrachromosomal DNA in lung cancer.Journal of the National Cancer Institute · 2026Article
- Phase separation of ecDNA condensates establishes in-trans contact domains that boost selective MYC regulatory interactions.Nature communications · 2026Article
- Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.Genome research · 2026Article
301 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
20 authors.
Hoon Kim *The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0003-4244-6126
Nam-Phuong Nguyen *Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Kristen TurnerLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
Sihan WuLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-8329-7492
Amit D GujarThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0003-0689-6680
Jens LuebeckDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-4391-979X
Jihe LiuThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-6111-1498
Viraj DeshpandeDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Utkrisht RajkumarDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
Sandeep NamburiThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Samirkumar B AminThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Eunhee YiThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0002-7839-7795
Francesca MenghiThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
Johannes H SchulteDepartment of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
Anton G HenssenDepartment of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0003-1534-778X
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-9459-4393
Christine R BeckThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.ORCID http://orcid.org/0000-0001-7821-8489
Paul S MischelLudwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA. pmischel@health.ucsd.edu.ORCID http://orcid.org/0000-0002-4560-2211
Vineet BafnaDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. vbafna@cs.ucsd.edu.ORCID http://orcid.org/0000-0002-5810-6241
Roel G W VerhaakThe Jackson Laboratory for Genomic Medicine, Farmington, CT, USA. roel.verhaak@jax.org.ORCID http://orcid.org/0000-0003-2773-0436
Funding
VIRAL MALIGNANCYP30CA023100 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DIANE M SIMEONE · 1985 to 2026
$124.9MShared Resource ManagementP30CA034196 · NCI · JACKSON LABORATORY · PI William Carl Skarnes · 1985 to 2026
$61.9MSpecial EquipmentP50HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2014 to 2018
$15.2MCenter for Personal Dynamic RegulomesRM1HG007735 · NHGRI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2019 to 2023
$13.8MLncRNA mechanisms in cancerR35CA209919 · NCI · STANFORD UNIVERSITY · PI CHANG, HOWARD Y · 2016 to 2022
$6.4MThe role of mTORC2 in reprogramming cancer cell metabolismR01NS073831 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI MISCHEL, PAUL S · 2011 to 2020
$3.4MComputational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2016 to 2026
$3.1MRepetitive sequences drive genome variation and plasticityR35GM133600 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Christine R Beck · 2019 to 2026
$3.0MExtrachromosomal DNA as a Targetable Mechanism in GlioblastomaR01CA237208 · NCI · YALE UNIVERSITY · PI VERHAAK, ROEL GW · 2020 to 2024
$2.5M(PQ #4) Single cell barcoding for studies of study clonal evolution in glioblastomaR01CA190121 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI SULMAN, ERIK, VERHAAK, ROEL GW · 2014 to 2017
$1.4MModeling Tumor Evolution in GliomaR21NS114873 · NINDS · JACKSON LABORATORY · PI VERHAAK, ROEL GW · 2019 to 2020
$520kHoward Hughes Medical InstituteNCI NIH HHS P30 CA023100NCI NIH HHS P30 CA034196NCI NIH HHS R01 CA190121NCI NIH HHS R01 CA237208NCI NIH HHS R35 CA209919NHGRI NIH HHS P50 HG007735NHGRI NIH HHS RM1 HG007735NIGMS NIH HHS R01 GM114362NIGMS NIH HHS R35 GM133600NINDS NIH HHS R01 NS073831NINDS NIH HHS R21 NS114873
Abstract
Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution
Indexed as
Cell Line, TumorChromatinChromosomesDNAGene AmplificationHumansNeoplasmsOncogenesChromatinDNA
Identifiers
What OpenQuestion holds
Textmetadata
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Read underepoch 390
Registered trials
NCT05827614ClinicalTrials.gov
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.