ArticleGenome medicine2021
Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients.
Article in Genome medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 45 citations in OpenAlex.
- Molecular residual disease assessment in colorectal and bladder cancer by somatic structural variant analysis of cell-free DNA whole-genome sequencing data.Journal of translational medicine · 2026Article
- Circulating Tumor DNA in Prostate Cancer: A Dual Perspective on Early Detection and Advanced Disease Management.Cancers · 2025Review
- Review
- Advancing precision oncology with AI-powered genomic analysis.Frontiers in pharmacology · 2025Review
- Uveal Melanoma: Comprehensive Review of Its Pathophysiology, Diagnosis, Treatment, and Future Perspectives.Biomedicines · 2024Review
- Leaf: an ultrafast filter for population-scale long-read SV detection.Genome biology · 2024Article
- Review
- Article
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- A survey of algorithms for the detection of genomic structural variants from long-read sequencing data.Nature methods · 2023Review
- Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis.Trends in analytical chemistry : TRAC · 2023Article
- Linked-read based analysis of the medulloblastoma genome.Frontiers in oncology · 2023Article
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- Bioinformatics roadmap for therapy selection in cancer genomics.Molecular oncology · 2022Review
- Is Tissue Still the Issue? The Promise of Liquid Biopsy in Uveal Melanoma.Biomedicines · 2022Review
- Application of long-read sequencing to the detection of structural variants in human cancer genomes.Computational and structural biotechnology journal · 2021Review
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons. These SVs could be quantified in ctDNA samples of patients with metastatic prostate cancer using a digital PCR assay. The results suggest that SV dynamics correlate with and may improve existing treatment-response biomarkers such as PSA. https://github.com/UMCUGenetics/SHARC .
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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.