ArticleProtein engineering, design & selection : PEDS2014
From deep sequencing to actual clones.
Article in Protein engineering, design & selection : PEDS, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Article
- Machine learning to predict continuous protein properties from binary cell sorting data and map unseen sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Position-Specific Enrichment Ratio Matrix scores predict antibody variant properties from deep sequencing data.Bioinformatics (Oxford, England) · 2023Article
- Direct selection of functional fluorescent-protein antibody fusions by yeast display.PloS one · 2023Article
- A Simple Whole-Plasmid PCR Method to Construct High-Diversity Synthetic Phage Display Libraries.Molecular biotechnology · 2022Article
- Generation of synthetic antibody fragments with optimal complementarity determining region lengths for Notch-1 recognition.Frontiers in microbiology · 2022Article
- Machine Learning-Guided Prediction of Antigen-Reactive In Silico Clonotypes Based on Changes in Clonal Abundance through Bio-Panning.Biomolecules · 2020Article
- High-Throughput Generation of In Silico Derived Synthetic Antibodies via One-step Enzymatic DNA Assembly of Fragments.Molecular biotechnology · 2020Article
- Advances in the Production and Batch Reformatting of Phage Antibody Libraries.Molecular biotechnology · 2019Review
- Next-generation sequencing-guided identification and reconstruction of antibody CDR combinations from phage selection outputs.Nucleic acids research · 2019Article
- Selection of phage-displayed accessible recombinant targeted antibodies (SPARTA): methodology and applications.JCI insight · 2018Article
- Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding.Frontiers in immunology · 2018Article
- Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering.Immunology · 2018Review
- Pacific Biosciences Sequencing and IMGT/HighV-QUEST Analysis of Full-Length Single Chain Fragment Variable from anFrontiers in immunology · 2017Article
- Platform for high-throughput antibody selection using synthetically-designed antibody libraries.New biotechnology · 2016Article
- Proteome-wide Identification of Novel Ceramide-binding Proteins by Yeast Surface cDNA Display and Deep Sequencing.Molecular & cellular proteomics : MCP · 2016Article
- Deep sequencing in library selection projects: what insight does it bring?Current opinion in structural biology · 2015Review
- Recombinant renewable polyclonal antibodies.mAbs · 2015Article
- One-Step Recovery of scFv Clones from High-Throughput Sequencing-Based Screening of Phage Display Libraries Challenged to Cells Expressing Native Claudin-1.BioMed research international · 2015Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The application of deep sequencing to in vitro display technologies has been invaluable for the straightforward analysis of enriched clones. After sequencing in vitro selected populations, clones are binned into identical or similar groups and ordered by abundance, allowing identification of those that are most enriched. However, the greatest strength of deep sequencing is also its greatest weakness: clones are easily identified by their DNA sequences, but are not physically available for testing without a laborious multistep process involving several rounds of polymerization chain reaction (PCR), assembly and cloning. Here, using the isolation of antibody genes from a phage and yeast display selection as an example, we show the power of a rapid and simple inverse PCR-based method to easily isolate clones identified by deep sequencing. Once primers have been received, clone isolation can be carried out in a single day, rather than two days. Furthermore the reduced number of PCRs required will reduce PCR mutations correspondingly. We have observed a 100% success rate in amplifying clones with an abundance as low as 0.5% in a polyclonal population. This approach allows us to obtain full-length clones even when an incomplete sequence is available, and greatly simplifies the subcloning process. Moreover, rarer, but functional clones missed by traditional screening can be easily isolated using this method, and the approach can be extended to any selected library (scFv, cDNA, libraries based on scaffold proteins) where a unique sequence signature for the desired clones of interest is available.
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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.