ArticleEMBO molecular medicine2023
Real-time analysis of the cancer genome and fragmentome from plasma and urine cell-free DNA using nanopore sequencing.
Article in EMBO molecular medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
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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.
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
40 citing papers in PubMed, 50 citations in OpenAlex.
- Advancing the applications of liquid biopsies in oncology.Nature reviews. Genetics · 2026Review
- Multi-omic cell free DNA profiles of cerebral spinal fluid from lung cancer metastasis to the brain.NAR cancer · 2026Article
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Near-perfect genome sequencing in medical genetics.Nature genetics · 2026Review
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Fragmentomics features of cell free DNA in eating disorders.Translational psychiatry · 2026Article
- Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer.Genome biology · 2026Article
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- Multidimensional liquid biopsy in bladder cancer: advances in circulating tumor cells, circulating tumor DNA, exosomes, and metabolomics.The oncologist · 2026Review
- A Comparative Review of Methods for Detecting Epidermal Growth Factor Receptor Mutations in Cell-free DNA from Lung Cancer Patients.Current molecular medicine · 2026Review
- Long-read sequencing for cancer liquid biopsy: advancing precision oncology.Frontiers in oncology · 2026Review
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Nanotechnology-Assisted Molecular Profiling: Emerging Advances in Circulating Tumor DNA Detection.International journal of nanomedicine · 2026Review
- The era of "Infectious Diseases+" has arrived: multi-disciplinary integration in pediatric infectious disease prevention and control.Frontiers in pediatrics · 2026Review
- Fragmenting the future with FLARE: a comprehensive fragmentomics pipeline based on long-read nanopore sequencing.Frontiers in genetics · 2026Article
- Circulating extracellular vesicle DNA (EV-DNA) and cell-free DNA in ovarian cancer: pathological relevance and diagnostic applications.Extracellular vesicles and circulating nucleic acids · 2026Review
- Peritoneal Lavage Cytology Predicts Peritoneal Metastasis and is Associated with Poor Prognosis in Patients with Stage II-III Colorectal Cancer.Annals of surgical oncology · 2025Article
- Urine cf-nucleosomes: A non-invasive window into human physiology and disease.Cell genomics · 2025Article
- Tracing the evolution of sequencing into the era of genomic medicine.Nature reviews. Genetics · 2025Review
- Circulating Tumor DNA detection in cancer: a comprehensive overview of current detection methods and prospects.The oncologist · 2025Review
Corrections and comments
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Authors and funding
17 authors at 2 institutions in 1 country.
Funding
Abstract
Cell-free DNA (cfDNA) can be isolated and sequenced from blood and/or urine of cancer patients. Conventional short-read sequencing lacks deployability and speed and can be biased for short cfDNA fragments. Here, we demonstrate that with Oxford Nanopore Technologies (ONT) sequencing we can achieve delivery of genomic and fragmentomic data from liquid biopsies. Copy number aberrations and cfDNA fragmentation patterns can be determined in less than 24 h from sample collection. The tumor-derived cfDNA fraction calculated from plasma of lung cancer patients and urine of bladder cancer patients was highly correlated (R = 0.98) with the tumor fraction calculated from short-read sequencing of the same samples. cfDNA size profile, fragmentation patterns, fragment-end composition, and nucleosome profiling near transcription start sites in plasma and urine exhibited the typical cfDNA features. Additionally, a high proportion of long tumor-derived cfDNA fragments (> 300 bp) are recovered in plasma and urine using ONT sequencing. ONT sequencing is a cost-effective, fast, and deployable approach for obtaining genomic and fragmentomic results from liquid biopsies, allowing the analysis of previously understudied cfDNA populations.
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Registered trials
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.