ArticleNucleic acids research2014
Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Next-Generation Sequencing Methods to Determine the Accuracy of Retroviral Reverse Transcriptases: Advantages and Limitations.Viruses · 2025Review
- Interpreting and de-noising genetically engineered barcodes in a DNA virus.PLoS computational biology · 2022Article
- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- Heritable tumor cell division rate heterogeneity induces clonal dominance.PLoS computational biology · 2018Article
- How low can we go? The implications of low bacterial load in respiratory microbiota studies.Pneumonia (Nathan Qld.) · 2018Review
- Analyzing Immunoglobulin Repertoires.Frontiers in immunology · 2018Review
- New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida).Ecology and evolution · 2017Article
- Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens.Scientific reports · 2017Article
- Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries.BMC genomics · 2017Article
- MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.PLoS computational biology · 2017Article
- Limitations and challenges of genetic barcode quantification.Scientific reports · 2017Article
- Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells.BMC bioinformatics · 2016Article
- Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting.Science advances · 2016Article
- Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse.PloS one · 2016Article
- High-fidelity target sequencing of individual molecules identified using barcode sequences: de novo detection and absolute quantitation of mutations in plasma cell-free DNA from cancer patients.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Deep sequencing in library selection projects: what insight does it bring?Current opinion in structural biology · 2015Review
- A bioinformatic framework for immune repertoire diversity profiling enables detection of immunological status.Genome medicine · 2015Article
- In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire.Frontiers in immunology · 2015Article
- Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice.BMC immunology · 2014Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Barcoded vectors are promising tools for investigating clonal diversity and dynamics in hematopoietic gene therapy. Analysis of clones marked with barcoded vectors requires accurate identification of potentially large numbers of individually rare barcodes, when the exact number, sequence identity and abundance are unknown. This is an inherently challenging application, and the feasibility of using contemporary next-generation sequencing technologies is unresolved. To explore this potential application empirically, without prior assumptions, we sequenced barcode libraries of known complexity. Libraries containing 1, 10 and 100 Sanger-sequenced barcodes were sequenced using an Illumina platform, with a 100-barcode library also sequenced using a SOLiD platform. Libraries containing 1 and 10 barcodes were distinguished from false barcodes generated by sequencing error by a several log-fold difference in abundance. In 100-barcode libraries, however, expected and false barcodes overlapped and could not be resolved by bioinformatic filtering and clustering strategies. In independent sequencing runs multiple false-positive barcodes appeared to be represented at higher abundance than known barcodes, despite their confirmed absence from the original library. Such errors, which potentially impact barcoding studies in an application-dependent manner, are consistent with the existence of both stochastic and systematic error, the mechanism of which is yet to be fully resolved.
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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.