ArticleNucleic acids research2020
Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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.
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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
27 citing papers in PubMed, 48 citations in OpenAlex.
- Post-Release Changes of the Goat's Rue Rhizobia (International journal of molecular sciences · 2026Article
- Bacterial Siderophore Production in Metal-Rich Environments: Underexplored Sources of Siderophores and Insights into Bioremediation.Journal of natural products · 2026Review
- Low power reprogrammable DNA basecaller with an efficient HMM accelerator for real time nanopore sequencing.Scientific reports · 2026Article
- Review
- Multilevel Gene Expression Changes in Lineages Containing Adaptive Copy Number Variants.Molecular biology and evolution · 2025Article
- Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.Genome biology and evolution · 2024Article
- Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection.Nature communications · 2024Article
- Comparing methylation levels assayed in GC-rich regions with current and emerging methods.BMC genomics · 2024Article
- Multilevel gene expression changes in lineages containing adaptive copy number variants.bioRxiv : the preprint server for biology · 2024Article
- A unifying model that explains the origins of human inverted copy number variants.PLoS genetics · 2024Review
- Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA.PLoS genetics · 2024Article
- Adapting Nanopore Sequencing Basecalling Models for Modification Detection via Incremental Learning and Anomaly Detection.bioRxiv : the preprint server for biology · 2023Article
- Comparative genomics analysis of three conserved plasmid families in the Western Hemisphere soft tick-borne relapsing fever borreliae provides insight into variation in genome structure and antigenic variation systems.Microbiology spectrum · 2023Article
- Copy number variation alters local and global mutational tolerance.Genome research · 2023Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution.Journal of molecular evolution · 2023Review
- Article
- Comparative genomics analysis of three conserved plasmid families in the Western Hemisphere soft tick-borne relapsing fever borreliae provides insight into variation in genome structure and antigenic variation systems.bioRxiv : the preprint server for biology · 2023Article
- Antigenic diversity in malaria parasites is maintained on extrachromosomal DNA.bioRxiv : the preprint server for biology · 2023Article
- Complex Genomic Rearrangements following Selection in a Glutamine-Limited Medium over Hundreds of Generations.Microbiology resource announcements · 2022Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Inverted duplicated DNA sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated DNA sequences using nanopore sequencing identified recurrent aberrant behavior characterized by low confidence, incorrect and missed base calls. Inverted duplicate DNA sequences in both yeast and human samples were observed to have systematic elevation in the electrical current detected at the nanopore, increased translocation rates and decreased sampling rates. The coincidence of inverted duplicated DNA sequences with dramatically reduced sequencing accuracy and an increased translocation rate suggests that secondary DNA structures may interfere with the dynamics of transit of the DNA through the nanopore.
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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.