ArticleNature genetics2023
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma.
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In one paragraph
Article in Nature genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 1 of them a synthesis that pooled it.
0numbers the graph read from it
0cells of the map it votes in
55citing papers in PubMed, 1 pooled it
13.9field-weighted citation impact, top 1% of its field
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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.
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Who cites it
55 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA.Frontiers in genetics · 2024Pooled it
- Extrachromosomal DNA as a platform for epigenetic reprogramming in cancer.Molecular cancer · 2026Review
- Extrachromosomal DNA in urothelial carcinoma: mechanisms and clinical applications.Nature reviews. Urology · 2026Review
- Multi-omics profiling of recurrence-associated extrachromosomal circular DNA characteristics and its prognostic potential in lung adenocarcinoma.Precision clinical medicine · 2026Article
- Plasticity of extrachromosomal DNA segregation during drug adaptation.Nature communications · 2026Article
- scAmp enables focal gene amplification analysis from single-cell data.Nature communications · 2026Article
- A Conserved Enhancer Locus in Extrachromosomal DNA and Homogeneously Staining Regions Activates MYC Transcription in Group 3 Medulloblastoma.Cancer research · 2026Article
- Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.Bioinformatics (Oxford, England) · 2026Article
- Cancer Heterogeneity and Cancer Cell Plasticity: Molecular Mechanisms and Precision Therapy.MedComm · 2026Review
- Beyond chromosomes: exploring the diverse functions of extrachromosomal circular DNA.Journal of advanced research · 2026Review
- Cis and trans regulatory mechanisms of extrachromosomal DNA segregation.Nature cell biology · 2026Article
- Preservation and clonal behavior of extrachromosomal DNA in patient-derived xenograft models of childhood cancers.Genome medicine · 2026Article
- The newfound relationship between extrachromosomal DNAs and excised signal circles.FEBS letters · 2026Review
- Targeting extrachromosomal DNA in human cancers.Nature reviews. Drug discovery · 2026Review
- Evolution of oncogene amplification across 86,000 cancer cell genomes.bioRxiv : the preprint server for biology · 2026Article
- Review
- Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.bioRxiv : the preprint server for biology · 2026Article
- Accurate prediction of ecDNA in interphase cancer cells using deep neural networks.Communications biology · 2026Article
- Functional role of small extrachromosomal circular DNA in colorectal cancer.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Plasma extrachromosomal circular DNA as a biomarker in EGFR-targeted therapy of non-small cell lung cancer.Molecular oncology · 2026Article
Corrections and comments
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Authors and funding
48 authors at 14 institutions in 2 countries.
Owen S ChapmanBioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA.
Jens LuebeckBioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA.
Sunita SridharDepartment of Medicine, University of California San Diego, San Diego, CA, USA.
Ivy Tsz-Lo WongDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-9761-3422
Deobrat DixitSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
Shanqing WangDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Gino PrasadDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Utkrisht RajkumarDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Meghana S PagadalaMedical Scientist Training Program, University of California San Diego, San Diego, CA, USA.ORCID 0000-0002-7591-6035
Jon D LarsonSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.ORCID 0000-0002-1570-695X
Britney Jiayu HeCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0001-8989-1521
King L HungCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0002-3662-4662
Joshua T LangeDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Siavash R DehkordiDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Sahaana ChandranSalk Institute for Biological Studies, La Jolla, CA, USA.
Miriam AdamDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
Ling MorganDepartment of Medicine, University of California San Diego, San Diego, CA, USA.
Sameena WaniSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
Ashutosh TiwariSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
Caitlin GuccioneBioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA.
Yingxi LinDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Aditi DuttaDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.
Yan Yuen LoSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
Edwin JuarezDepartment of Medicine, University of California San Diego, San Diego, CA, USA.
James T RobinsonDepartment of Medicine, University of California San Diego, San Diego, CA, USA.
Andrey KorshunovClinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 280, Heidelberg, Germany.
John-Edward A MichaelsPapé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA.
Yoon-Jae ChoPapé Pediatric Research Institute, Department of Pediatrics and Knight Cancer Insitute, Oregon Health and Sciences University, Portland, OR, USA.
Denise M MalickiDivision of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA.
Nicole G CoufalDepartment of Pediatrics, UC San Diego and Rady Children's Hospital, San Diego, CA, USA.ORCID 0000-0001-6547-1733
Michael L LevyDivision of Pathology, UC San Diego and Rady Children's Hospital, San Diego, CA, USA.
Charlotte HobbsRady Children's Institute for Genomic Medicine, Rady Children's Hospital and Healthcare Center, San Diego, CA, USA.
Richard H ScheuermannJ. Craig Venter Institute, La Jolla, CA, USA.
John R CrawfordDepartment of Pediatrics, University of California Irvine and Children's Hospital Orange County, Irvine, CA, USA.
Scott L PomeroyEli and Edythe Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Jeremy N RichUPMC Hillman Cancer Center, Pittsburgh, PA, USA.
Xinlian ZhangDivision of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, San Diego, CA, USA.
Howard Y ChangCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.ORCID 0000-0002-9459-4393
Jesse R DixonSalk Institute for Biological Studies, La Jolla, CA, USA.ORCID 0000-0002-6273-2181
Anindya BagchiSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.
Aniruddha J DeshpandeSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.ORCID 0000-0002-5240-9356
Hannah CarterDepartment of Medicine, University of California San Diego, San Diego, CA, USA.ORCID 0000-0002-1729-2463
Ernest FraenkelDepartment of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID 0000-0001-9249-8181
Paul S MischelDepartment of Pathology, Stanford University School of Medicine, Stanford, CA, USA.ORCID 0000-0002-4560-2211
Robert J Wechsler-ReyaSanford Burnham Prebys Medical Discovery Institute, San Diego, CA, USA.ORCID 0000-0002-7463-8352
Vineet BafnaDepartment of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA.ORCID 0000-0002-5810-6241
Jill P MesirovDepartment of Medicine, University of California San Diego, San Diego, CA, USA.ORCID 0000-0002-9755-2818
Lukas ChavezDepartment of Medicine, University of California San Diego, San Diego, CA, USA. lchavez@sbpdiscovery.org.ORCID 0000-0002-8718-8848
University of California San Diego · USSanford Burnham Prebys Medical Discovery Institute · USStanford University · USChildren’s Institute · USBroad Institute · USOregon Health & Science University · USSalk Institute for Biological Studies · USChildren's Hospital of Orange County · USGerman Cancer Research Center · DEHoward Hughes Medical Institute · USJ. Craig Venter Institute · USMassachusetts Institute of Technology · USUniversity of Pittsburgh · USUniversity of San Diego · US
Funding
VIRAL MALIGNANCYP30CA023100 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DIANE M SIMEONE · 1985 to 2026
$124.9MTumor Microenvironment and Cancer ImmunologyP30CA030199 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI ELENA B PASQUALE · 1985 to 2026
$107.2MMouse models to discover new drivers of medulloblastomaR01CA159859 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Michael D. Taylor, WILLIAM A WEISS · 2011 to 2026
$10.4MSan Diego Biomedical Informatics Education & Research (SABER)T15LM011271 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHAMIM NEMATI · 2012 to 2026
$9.7MU of Calif, San Diego Neuroscience Microscopy ImagingP30NS047101 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GLEESON, JOSEPH G, ZHENG, BINHAI · 2003 to 2022
$9.0MeDyNAmiC - STANFORDOT2CA278688 · NCI · STANFORD UNIVERSITY · PI PAUL S MISCHEL · 2022 to 2026
$7.7MSupporting Integrative Genomic Analysis Users with GenePatternR01GM074024 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2005 to 2019
$6.6MThe Integrative Genomics Viewer (IGV) for Cancer ResearchU24CA258406 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JILL P. MESIROV, James Thomas Robinson · 2021 to 2026
$5.1MThe Integrative Genomics Viewer (IGV): visualization supporting cancer researchU24CA210004 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P., ROBINSON, JAMES THOMAS · 2016 to 2020
$3.8MEmbryonal Brain Tumor NetworksU01CA184898 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI FRAENKEL, ERNEST, MESIROV, JILL P. · 2014 to 2019
$3.6MIdentifying and Targeting the Drivers of Pediatric Brain TumorsR35NS122339 · NINDS · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Robert J. Wechsler-Reya · 2021 to 2026
$3.6MSoftware and algorithms for elucidating the structure, function, and evolution of extrachromosomal DNAU24CA264379 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, MESIROV, JILL P. · 2021 to 2025
$3.5MCancer Research UK CGCATF-2021/100012NCI NIH HHS F31 CA271777NCI NIH HHS F99 CA274692NCI NIH HHS OT2 CA278635NCI NIH HHS OT2 CA278688NCI NIH HHS P30 CA023100NCI NIH HHS R01 CA159859NCI NIH HHS R01 CA238249NCI NIH HHS R01 CA238379NCI NIH HHS U01 CA184898NCI NIH HHS U01 CA253547NCI NIH HHS U24 CA210004NCI NIH HHS U24 CA220341NCI NIH HHS U24 CA258406NCI NIH HHS U24 CA264379NIGMS NIH HHS R01 GM074024NIGMS NIH HHS R01 GM114362NINDS NIH HHS P30 NS047101NINDS NIH HHS R01 NS132780NINDS NIH HHS R21 NS116455NINDS NIH HHS R21 NS120075NINDS NIH HHS R21 NS130137NINDS NIH HHS R35 NS122339NLM NIH HHS T15 LM011271
Abstract
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.
Indexed as
Cerebellar NeoplasmsMedulloblastomaNeoplasmsDNA, CircularHumansOncogenesRetrospective StudiesDNA, Circular
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