ArticleScientific reports2014
Non-random DNA fragmentation in next-generation sequencing.
Article in Scientific reports, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Enhancing DNA recovery in low-biomass snow algae samples: a comparative study of extraction methods and their effect on community composition.Applied and environmental microbiology · 2026Article
- Sequence bias in chromatin fragmentation leads to misinterpretation of protein-DNA interactions in vivo.Genome biology · 2026Article
- Strong bias in long-read sequencing prevents assembly ofGenome research · 2026Article
- GelInsight: Open-source software for large-sample DNA fragmentation quality control in gel electrophoresis images.PloS one · 2026Article
- Article
- Prior knowledge on context-driven DNA fragmentation probabilities can improve de novo genome assembly algorithms.BMC bioinformatics · 2025Article
- Mapping-based genome size estimation.BMC genomics · 2025Article
- A rapid and efficient zirconia bead-mediated ultrasonic strategy for DNA fragmentation up to 10 kbp.RSC advances · 2025Article
- Article
- Sequencing and Optical Genome Mapping for the Adventurous Chemist.Chemical & biomedical imaging · 2024Review
- Genomic analyses elucidateEcology and evolution · 2024Article
- Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs.International journal of molecular sciences · 2023Article
- Retinitis Pigmentosa: Current Clinical Management and Emerging Therapies.International journal of molecular sciences · 2023Review
- Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones.Genetics · 2023Article
- Article
- Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules.PloS one · 2023Article
- Cell-type specific profiling of histone post-translational modifications in the adult mouse striatum.Nature communications · 2022Article
- Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis.Scientific reports · 2022Article
- The enhancement of DNA fragmentation in a bench top ultrasonic water bath with needle-induced air bubbles: Simulation and experimental investigation.Biomicrofluidics · 2022Article
- Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed "reads" are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA breaks are random and sequence-independent. However, previously we showed that for the sonicated restriction DNA fragments the rates of double-stranded breaks depend on the nucleotide sequence. In this work we analyzed genomic reads from NGS data and discovered that fragmentation methods based on the action of the hydrodynamic forces on DNA, produce similar bias. Consideration of this non-random DNA fragmentation may allow one to unravel what factors and to what extent influence the non-uniform coverage of various genomic regions.
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Registered trials
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