ArticleNature communications2024
Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Extrachromosomal Circular DNA May Contribute to Histopathologic Characteristics in Esophageal Combined Basaloid Squamous Cell Carcinoma.Annals of surgical oncology · 2026Article
- Extrachromosomal DNA as a platform for epigenetic reprogramming in cancer.Molecular cancer · 2026Review
- Pan-cancer analysis identifies immunoproteasome as the predominant survival-associated component of antigen processing machinery.Translational oncology · 2026Article
- Tumorigenesis of well-differentiated and dedifferentiated liposarcoma: 12q amplicon architecture, oncogenic cargo, and evolutionary progression.Cancer metastasis reviews · 2026Review
- A bibliometric analysis of extrachromosomal DNA in cancer over six decades.Discover oncology · 2026Article
- Targeting extrachromosomal DNA in human cancers.Nature reviews. Drug discovery · 2026Review
- Integrating single-cell and bulk transcriptomes to reveal prognostic and immunological features of ecDNA-related genes in osteosarcoma.Cancer immunology, immunotherapy : CII · 2026Article
- Accurate prediction of ecDNA in interphase cancer cells using deep neural networks.Communications biology · 2026Article
- Exploring promising biomarkers based on pathogenic mechanisms in interstitial cystitis/bladder pain syndrome.Nature reviews. Urology · 2026Review
- Artificial intelligence models: transforming early diagnosis and precise treatment of gastrointestinal cancers.Molecular cancer · 2026Review
- Extrachromosomal DNA drives molecular and clinical heterogeneity in hepatocellular carcinoma: a multi-omics analysis and prognostic model development.Human genomics · 2026Article
- Extrachromosomal DNA and cancer: function, formation, and clinical implications.Journal of experimental & clinical cancer research : CR · 2026Review
- Loss of KDM6A-mediated genomic instability and metabolic reprogramming regulates response to therapeutic perturbations in bladder cancer.Nature communications · 2026Article
- Clinicopathological and genomic features of extrachromosomal DNA in gastric cancer.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- Profiling Extrachromosomal Circular DNA (ecDNA) in CancerAnti-cancer agents in medicinal chemistry · 2026Review
- Machine learning identified extrachromosomal DNA-related 12 gene signatures to predict cancer immunotherapy response.Cancer cell international · 2025Article
- Trends in artificial intelligence and machine learning for renal cancer.Discover oncology · 2025Article
- Leveraging artificial intelligence and machine learning in kinase inhibitor development: advances, challenges, and future prospects.RSC medicinal chemistry · 2025Review
- Extrachromosomal Circular DNA as a Cancer Biomarker: From Diagnosis to Treatment.Cancer innovation · 2025Review
- Research Advances of Extrachromosomal Circular DNA in Breast Cancer.Cancer medicine · 2025Review
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The clinical implications of extrachromosomal DNA (ecDNA) in cancer therapy remain largely elusive. Here, we present a comprehensive analysis of ecDNA amplification spectra and their association with clinical and molecular features in multiple cohorts comprising over 13,000 pan-cancer patients. Using our developed computational framework, GCAP, and validating it with multifaceted approaches, we reveal a consistent pan-cancer pattern of mutual exclusivity between ecDNA amplification and microsatellite instability (MSI). In addition, we establish the role of ecDNA amplification as a risk factor and refine genomic subtypes in a cohort from 1015 colorectal cancer patients. Importantly, our investigation incorporates data from four clinical trials focused on anti-PD-1 immunotherapy, demonstrating the pivotal role of ecDNA amplification as a biomarker for guiding checkpoint blockade immunotherapy in gastrointestinal cancer. This finding represents clinical evidence linking ecDNA amplification to the effectiveness of immunotherapeutic interventions. Overall, our study provides a proof-of-concept of identifying ecDNA amplification from cancer whole-exome sequencing (WES) data, highlighting the potential of ecDNA amplification as a valuable biomarker for facilitating personalized cancer treatment.
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