ArticleCancer biology & therapy2016
Nanopore sequencing detects structural variants in cancer.
Article in Cancer biology & therapy, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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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.
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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
79 citing papers in PubMed.
- Long-read genome sequencing resolves the breakpoints of a chromosome 8;22 balanced translocation in NF2-related schwannomatosis.Scientific reports · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Review
- Nanopore adaptive sampling to identify the NLR gene family in melon (Cucumis melo L.).BMC genomics · 2025Article
- The Cancer Genome in the Long Reads Era.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Nanopore sequencing in veterinary medicine: from concepts to clinical applications.Frontiers in cellular and infection microbiology · 2025Review
- Leveraging the power of long reads for targeted sequencing.Genome research · 2024Review
- Tissue and Plasma-Based Highly Sensitive Blocker Displacement Amplicon Nanopore Sequencing for EGFR Mutations in Lung Cancer.Cancer research and treatment · 2024Article
- The Application of Long-Read Sequencing to Cancer.Cancers · 2024Review
- CRISPR-Cas9-guided amplification-free genomic diagnosis for familial hypercholesterolemia using nanopore sequencing.PloS one · 2024Article
- Beyond assembly: the increasing flexibility of single-molecule sequencing technology.Nature reviews. Genetics · 2023Review
- The application of long-read sequencing in clinical settings.Human genomics · 2023Review
- Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing.Sensors (Basel, Switzerland) · 2023Article
- Detection of Biological Molecules Using Nanopore Sensing Techniques.Biomedicines · 2023Review
- Review
- Resolving complex structural variants via nanopore sequencing.Frontiers in genetics · 2023Review
- Portable nanopore-sequencing technology: Trends in development and applications.Frontiers in microbiology · 2023Review
- Article
- Comprehensive analysis and accurate quantification of unintended large gene modifications induced by CRISPR-Cas9 gene editing.Science advances · 2022Article
- Typical Enhancers, Super-Enhancers, and Cancers.Cancers · 2022Review
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300 bp) of 2nd generation sequencing. Not only do the reads (or paired-end reads) need to straddle a breakpoint, but repetitive elements often lead to ambiguities in the alignment of short reads. We propose to use the long-reads (up to 20 kb) possible with 3rd generation sequencing, specifically nanopore sequencing on the MinION. Nanopore sequencing relies on a similar concept to a Coulter counter, reading the DNA sequence from the change in electrical current resulting from a DNA strand being forced through a nanometer-sized pore embedded in a membrane. Though nanopore sequencing currently has a relatively high mismatch rate that precludes base substitution and small frameshift mutation detection, its accuracy is sufficient for SV detection because of its long reads. In fact, long reads in some cases may improve SV detection efficiency. We have tested nanopore sequencing to detect a series of well-characterized SVs, including large deletions, inversions, and translocations that inactivate the CDKN2A/p16 and SMAD4/DPC4 tumor suppressor genes in pancreatic cancer. Using PCR amplicon mixes, we have demonstrated that nanopore sequencing can detect large deletions, translocations and inversions at dilutions as low as 1:100, with as few as 500 reads per sample. Given the speed, small footprint, and low capital cost, nanopore sequencing could become the ideal tool for the low-level detection of cancer-associated SVs needed for molecular relapse, early detection, or therapeutic monitoring.
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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.