ArticleNPJ precision oncology2023
Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients.
Article in NPJ precision oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Survival prediction landscape: an in-depth systematic literature review on activities, methods, tools, diseases, and databases.Frontiers in artificial intelligence · 2024Pooled it
- Phase II Trial of Risk-Enabled Therapy After Neoadjuvant Chemotherapy for Muscle-Invasive Bladder Cancer (RETAIN 1).Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2025Trial
- CRISPR-Scan: Cas13a Mismatch Tolerance Enabled Ultra-Multiplexed Detection of Same-Site Indels in Acute Myeloid Leukemia.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Urinary Biomarkers in Urological Oncology: From Biological Origin to Clinical Decision-Making-A Narrative Review.Diagnostics (Basel, Switzerland) · 2026Review
- ctDNA Dynamics and Recurrence Patterns after Organ-Sparing Trimodality Therapy for Bladder Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- From feasibility to translational pathways: a bibliometric and knowledge-mapping analysis of urine-based liquid biopsy in urologic cancers (2015-2025).Journal of translational medicine · 2026Review
- Review
- Detection of mutated KRAS, TP53, CDKN2A, and SMAD4 in tumor cell-free DNA of Brazilian pancreatic adenocarcinoma patients using next-generation sequencing.Scientific reports · 2026Article
- Deep learning-based non-invasive profiling of tumor transcriptomes from cell-free DNA for precision oncology.bioRxiv : the preprint server for biology · 2026Article
- Postoperative Lymph Is a Proximal Source of ctDNA for Detection of Recurrence in HPV-Independent Head and Neck Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Emerging Molecular and Computational Biomarkers in Urothelial Carcinoma: Innovations in Diagnosis, Prognosis, and Therapeutic Response Prediction.Journal of personalized medicine · 2026Review
- Prediction of Postoperative Intravesical Recurrence Using Urine DNA Monitoring in Nonmuscular-Invasive Urothelial Bladder Cancer.International journal of urology : official journal of the Japanese Urological Association · 2026Article
- Progress in the application of combined detection of urinary tumor DNA and exosomes in the classification, staging, and clinical management of bladder cancer: a review.Frontiers in oncology · 2026Review
- Emerging technologies and clinical translation of urine-based liquid biopsy in urological cancers.Genes & genomics · 2025Review
- Current Status and Future Perspectives of Molecular Residual Disease Testing in Genitourinary Cancers.International journal of urology : official journal of the Japanese Urological Association · 2025Review
- Liquid biopsies across the cancer care continuum.Nature medicine · 2025Review
- Circulating-free DNA: A promising tool for early detection of myocardial infarction.International journal of cardiology. Cardiovascular risk and prevention · 2025Review
- T cell subsets of urine-derived lymphocytes (UDLs) serve as an indicator of TILs and reflect immunological sex differences in bladder cancer.Journal for immunotherapy of cancer · 2025Article
- The 3PM transformation potential of minimal residual disease in solid tumor management: a bibliometric analysis and review.The EPMA journal · 2025Review
- Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities.Molecular oncology · 2025Review
Corrections and comments
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Authors and funding
21 authors at 5 institutions in 1 country.
Funding
Abstract
Circulating tumor DNA (ctDNA) sensitivity remains subpar for molecular residual disease (MRD) detection in bladder cancer patients. To remedy this problem, we focused on the biofluid most proximal to the disease, urine, and analyzed urine tumor DNA in 74 localized bladder cancer patients. We integrated ultra-low-pass whole genome sequencing (ULP-WGS) with urine cancer personalized profiling by deep sequencing (uCAPP-Seq) to achieve sensitive MRD detection and predict overall survival. Variant allele frequency, inferred tumor mutational burden, and copy number-derived tumor fraction levels in urine cell-free DNA (cfDNA) significantly predicted pathologic complete response status, far better than plasma ctDNA was able to. A random forest model incorporating these urine cfDNA-derived factors with leave-one-out cross-validation was 87% sensitive for predicting residual disease in reference to gold-standard surgical pathology. Both progression-free survival (HR = 3.00, p = 0.01) and overall survival (HR = 4.81, p = 0.009) were dramatically worse by Kaplan-Meier analysis for patients predicted by the model to have MRD, which was corroborated by Cox regression analysis. Additional survival analyses performed on muscle-invasive, neoadjuvant chemotherapy, and held-out validation subgroups corroborated these findings. In summary, we profiled urine samples from 74 patients with localized bladder cancer and used urine cfDNA multi-omics to detect MRD sensitively and predict survival accurately.
Identifiers
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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.