ArticleCell2020
Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.
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In one paragraph
Article in Cell, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 172 papers.
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172citing papers in PubMed
–field-weighted citation impact
What it found
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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.
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Who cites it
172 citing papers in PubMed.
- How telomere attrition protects against cancer.Nature reviews. Genetics · 2026Review
- Unraveling the lexicon of complex mutational phenomena in human cancers.Nature cancer · 2026Review
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- Molecular pathology in the diagnosis of cutaneous melanoma.Pathologie (Heidelberg, Germany) · 2026Review
- Article
- Examining the role of extrachromosomal DNA in lung cancer.Journal of the National Cancer Institute · 2026Article
- A High-Fidelity and Ancestrally Inclusive Patient-Derived Organoid Platform Resolves Cancer Cell Plasticity in Uterine Carcinosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Detecting and reconstructing breakage-fusion-bridge cycles from long-read sequencing using BFBArchitect.Bioinformatics (Oxford, England) · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Tumor genome and microenvironment alteration by trastuzumab deruxtecan as neoadjuvant therapy for HER2-mutant NSCLC.Scientific reports · 2026Article
- Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally Diverse Cohort.bioRxiv : the preprint server for biology · 2026Article
- Convergent evolution of complex structural variants drives therapy resistance in metastatic prostate cancer.Genome biology · 2026Article
- Esophageal cancer: from pathogenesis to precision therapies.Signal transduction and targeted therapy · 2026Review
- 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
- Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort.NPJ genomic medicine · 2026Article
- Chromosomal instability shapes the tumor microenvironment of esophageal adenocarcinoma via a cGAS-chemokine-myeloid axis.Science advances · 2026Article
- Telomere Crisis Shapes Cancer Evolution.Cold Spring Harbor perspectives in biology · 2026Review
- Cross-Species Exome Sequencing Reveals Recurrent Genomic Alterations in California Sea Lion (Genes · 2026Article
- Integrated mutational landscape analysis of endometrial stromal sarcoma.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
112 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
52 authors.
Kevin HadiDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA.
Xiaotong YaoDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Julie M BehrDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Aditya DeshpandeDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Charalampos XanthopoulakisDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Huasong TianDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA.
Sarah KudmanDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Joel RosieneDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA.
Madison DarmofalDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Joseph DeRoseNew York Genome Center, New York, NY 10013, USA.
Rick MortensenNew York Genome Center, New York, NY 10013, USA.
Emily M AdneyDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA.
Alon ShaiberDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Zoran GajicNew York Genome Center, New York, NY 10013, USA.
Michael SigourosEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Kenneth EngEnglander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
Jeremiah A WalaBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Kazimierz O WrzeszczyńskiNew York Genome Center, New York, NY 10013, USA.
Kanika AroraNew York Genome Center, New York, NY 10013, USA.
Minita ShahNew York Genome Center, New York, NY 10013, USA.
Anne-Katrin EmdeNew York Genome Center, New York, NY 10013, USA.
Vanessa FeliceNew York Genome Center, New York, NY 10013, USA.
Mayu O FrankNew York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
Robert B DarnellNew York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
Mahmoud GhandiBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Franklin HuangBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Sally DewhurstLaboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA.
John MaciejowskiDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Titia de LangeLaboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA.
Jeremy SettonDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Nadeem RiazDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Jorge S Reis-FilhoHuman Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Simon PowellDepartment of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
David A KnowlesNew York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10027, USA.
Ed ReznikDepartment of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Bud MishraDepartments of Computer Science, Mathematics and Cell Biology, Courant Institute and NYU School of Medicine, New York University, New York, NY 10012, USA.
Rameen BeroukhimBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Michael C ZodyNew York Genome Center, New York, NY 10013, USA.
Nicolas RobineNew York Genome Center, New York, NY 10013, USA.
Kenji M OmanDivisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Carissa A SanchezDivisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Mary K KuhnerDepartment of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Lucian P SmithDepartment of Bioengineering, University of Washington, Seattle, WA 98195, USA.
Patricia C GalipeauDivisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Thomas G PaulsonDivisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Brian J ReidDivisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Xiaohong LiDivisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
David WilkesDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Andrea SbonerDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
Juan Miguel MosqueraDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
Olivier ElementoDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
Marcin ImielinskiDepartment of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA. Electronic address: mski@mskilab.org.
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Nicholas D Socci · 1985 to 2026
$347.4MTranslational Bioimaging Core Shared ResourceP30CA015704 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI Marian Esvelt · 1985 to 2026
$296.4MPHYLOGENIES of Barrett's Esophagus LineagesP01CA091955 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI GRADY, WILLIAM MALLORY · 2002 to 2019
$35.9MTransforming Translational Science and Education to Benefit Human HealthUL1TR000043 · NCATS · ROCKEFELLER UNIVERSITY · PI COLLER, BARRY · 2012 to 2015
$26.8MTargeting Polθ to Overcome PARP Inhibitor Resistance in Homologous Recombination Deficient Breast CancerP50CA247749 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI Sarat Chandarlapaty, Simon N. Powell · 2020 to 2026
$16.3MTraining Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8MTopology of Cancer Evolution and HeterogeneityU54CA193313 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI IAVARONE, ANTONIO, RABADAN, RAUL · 2015 to 2020
$10.4MCombining New Molecular and Informatic Strategies to Find Hidden Ways to Treat Brain DiseaseR35NS097404 · NINDS · ROCKEFELLER UNIVERSITY · PI DARNELL, ROBERT B · 2017 to 2024
$9.0MTri-Institutional PhD Program in Computational Biology & MedicineT32GM132083 · NIGMS · WEILL MEDICAL COLL OF CORNELL UNIV · PI Doron Betel, Iman Hajirasouliha · 2020 to 2026
$3.6MThe identification and validation of mechanisms and biomarkers for relapse in diffuse large B-cell lymphoma (Administrative Supplement)R01CA194547 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI ELEMENTO, OLIVIER, TAM, WAYNE · 2015 to 2019
$2.6MThe joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor ProfilesU24CA210989 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI ELEMENTO, OLIVIER, ZODY, MICHAEL C · 2016 to 2020
$2.4MTowards a Simulation of Cancer Genomes for Benchmarking Structural Variant AlgorithmsF31CA232465 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI HADI, KEVIN MATTHEW · 2018 to 2020
$135kHoward Hughes Medical InstituteNCATS NIH HHS UL1 TR000043NCI NIH HHS F31 CA232465NCI NIH HHS P01 CA091955NCI NIH HHS P30 CA008748NCI NIH HHS P30 CA015704NCI NIH HHS P50 CA247749NCI NIH HHS R01 CA194547NCI NIH HHS U24 CA210989NCI NIH HHS U54 CA193313NHGRI NIH HHS T32 HG002295NIGMS NIH HHS T32 GM132083NINDS NIH HHS R35 NS097404
Abstract
Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.
Indexed as
Chromosome InversionChromothripsisDNA Copy Number VariationsGene RearrangementGenome, HumanGenomicsGenomic Structural VariationHumansMutationNeoplasmsWhole Genome Sequencinganeuploidycancer evolutioncancer genomicschromothripsisfragile sitesgenome graphsmutational processesphasingstructural variationsuperenhancers
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