ArticleNucleic acids research2021
High resolution copy number inference in cancer using short-molecule nanopore sequencing.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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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
15 citing papers in PubMed.
- ComplexInternational journal of molecular sciences · 2026Review
- Technical feasibility of a long read, fourth generation sequencing platform in diagnostic profiling of clinical routine samples: a proof-of-concept study.Pathologica · 2026Article
- The transformative impact of ultra-rapid nanopore sequencing in precision medicine.Frontiers in immunology · 2026Review
- Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.Frontiers in neurology · 2026Article
- Review
- Application and Prospects of Long-Read Sequencers for Preimplantation Genetic Testing for Structural Rearrangements.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Considering Biomarkers of Neurodegeneration in Alzheimer's Disease: The Potential of Circulating Cell-Free DNA in Precision Neurology.Journal of personalized medicine · 2024Review
- Oxford Nanopore Technology and its Application in Liquid Biopsies.Current genomics · 2023Review
- Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer.NAR cancer · 2023Article
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- Transcriptome profiling for precision cancer medicine using shallow nanopore cDNA sequencing.Scientific reports · 2023Article
- Resolving complex structural variants via nanopore sequencing.Frontiers in genetics · 2023Review
- Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing.Genome biology · 2022Article
- Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Genome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for broader clinical utility, for example in smaller hospitals, due to lower instrument cost, higher portability, and ease of use. Nonetheless, Nanopore sequencing devices are limited in the number of retrievable sequencing reads/molecules compared to short-read sequencing platforms, limiting CNA inference accuracy. To address this limitation, we targeted the sequencing of short-length DNA molecules loaded at optimized concentration in an effort to increase sequence read/molecule yield from a single nanopore run. We show that short-molecule nanopore sequencing reproducibly returns high read counts and allows high quality CNA inference. We demonstrate the clinical relevance of this approach by accurately inferring CNAs in acute myeloid leukemia samples. The data shows that, compared to traditional approaches such as chromosome analysis/cytogenetics, short molecule nanopore sequencing returns more sensitive, accurate copy number information in a cost effective and expeditious manner, including for multiplex samples. Our results provide a framework for short-molecule nanopore sequencing with applications in research and medicine, which includes but is not limited to, CNAs.
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Registered trials
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