ArticleGenome biology2017
Characterization of background noise in capture-based targeted sequencing data.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Utility of targeted deep sequencing for detecting circulating tumor DNA in pancreatic cancer patients.Scientific reports · 2018Trial
- Benchmarking Q40 sequencing for sensitive and efficient detection of rare genomic variants.Genome biology · 2026Article
- A compendium of horizontal gene transfers in Metazoa.Scientific data · 2026Article
- Liquid biopsy in lung cancer screening: rationale, progress, opportunities and challenges.Clinical and experimental medicine · 2025Review
- The eukaryotic horizontal gene transfer dataset a compendium.bioRxiv : the preprint server for biology · 2025Article
- Correlation between variant allele frequency and mean tumor molecules with tumor burden in patients with solid tumors.Molecular oncology · 2024Article
- Effect of sequencing platforms on the sensitivity of chemical mutation detection using Hawk-Seq™.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2024Article
- Characterization and mitigation of artifacts derived from NGS library preparation due to structure-specific sequences in the human genome.BMC genomics · 2024Article
- Islands of genomic stability in the face of genetically unstable metastatic cancer.bioRxiv : the preprint server for biology · 2024Article
- Article
- Validation of genetic variants from NGS data using deep convolutional neural networks.BMC bioinformatics · 2023Article
- Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment.Frontiers in genetics · 2023Review
- Circulating cell-free DNA for cancer early detection.Innovation (Cambridge (Mass.)) · 2022Review
- Colorectal Cancer Is Associated with the Presence of Cancer Driver Mutations in Normal Colon.Cancer research · 2022Article
- An improved molecular inversion probe based targeted sequencing approach for low variant allele frequency.NAR genomics and bioinformatics · 2022Article
- Direct comparison of circulating tumor DNA sequencing assays with targeted large gene panels.PloS one · 2022Article
- Impact of Low-BurdenFrontiers in oncology · 2022Review
- Single-strand specific nuclease enhances accuracy of error-corrected sequencing and improves rare mutation-detection sensitivity.Archives of toxicology · 2022Article
- Internal validation and improvement of mitochondrial genome sequencing using the Precision ID mtDNA Whole Genome Panel.International journal of legal medicine · 2021Article
- noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise.Nucleic acids research · 2021Article
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTargeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred during specific steps of the capture-based targeted sequencing process.
resultsWe removed most sequencing artifacts by filtering out low-quality bases and then analyze the remaining background noise. By recognizing that plasma DNA is naturally fragmented to be of a size comparable to that of mono-nucleosomal DNA, we were able to identify and characterize errors that are specifically associated with acoustic shearing. Two-thirds of C:G > A:T errors and one quarter of C:G > G:C errors were attributed to the oxidation of guanine during acoustic shearing, and this was further validated by comparative experiments conducted under different shearing conditions. The acoustic shearing step also causes A > G and A > T substitutions localized to the end bases of sheared DNA fragments, indicating a probable association of these errors with DNA breakage. Finally, the hybrid selection step contributes to one-third of the remaining C:G > A:T and one-fifth of the C > T errors.
conclusionsThe results of this study provide a comprehensive summary of various errors incurred during targeted deep sequencing, and their underlying causes. This information will be invaluable to drive technical improvements in this sequencing method, and may increase the future usage of targeted deep sequencing methods for low-allelic fraction variant detection.
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