ArticleNucleic acids research2014
An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage.
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 76 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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Who cites it
76 citing papers in PubMed, 132 citations in OpenAlex.
- DisTAL-Seq: A TALEN-specific adaptation of DISCOVER-Seq for off-target profiling.Molecular therapy. Nucleic acids · 2026Article
- Multi-targeting zinc finger nuclease vector unsilences paternal UBE3A in a mouse model of Angelman syndrome.Gene therapy · 2026Article
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- Artificial Intelligence and Computational Biology in Gene Therapy: A Review.Biochemical genetics · 2025Review
- Engineering with care: safety assessment platforms for CRISPR-modified natural killer cells.Frontiers in immunology · 2025Review
- Corneal gene therapy: Structural and mechanistic understanding.The ocular surface · 2023Article
- Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells.Scientific reports · 2023Article
- Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities.International journal of molecular sciences · 2023Review
- T-CAST: An optimized CAST-Seq pipeline for TALEN confirms superior safety and efficacy of obligate-heterodimeric scaffolds.Frontiers in genome editing · 2023Article
- CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA.Nature biotechnology · 2022Article
- Genome Editing With TALEN, CRISPR-Cas9 and CRISPR-Cas12a in Combination With AAV6 Homology Donor Restores T Cell Function for XLP.Frontiers in genome editing · 2022Article
- The comparison of ZFNs, TALENs, and SpCas9 by GUIDE-seq in HPV-targeted gene therapy.Molecular therapy. Nucleic acids · 2021Article
- LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy.The EMBO journal · 2021Article
- Improved Specificity and Safety of Anti-Hepatitis B Virus TALENs Using Obligate HeterodimericViruses · 2021Article
- Automated generation of gene-edited CAR T cells at clinical scale.Molecular therapy. Methods & clinical development · 2021Article
- Tools for experimental and computational analyses of off-target editing by programmable nucleases.Nature protocols · 2021Review
- Epigenome engineering: new technologies for precision medicine.Nucleic acids research · 2020Article
- Plant Genome Editing and the Relevance of Off-Target Changes.Plant physiology · 2020Article
- iPSC-Derived Intestinal Organoids from Cystic Fibrosis Patients Acquire CFTR Activity upon TALEN-Mediated Repair of the p.F508del Mutation.Molecular therapy. Methods & clinical development · 2020Article
- Genome Editing of theCells · 2020Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Although engineered nucleases can efficiently cleave intracellular DNA at desired target sites, major concerns remain on potential 'off-target' cleavage that may occur throughout the genome. We developed an online tool: predicted report of genome-wide nuclease off-target sites (PROGNOS) that effectively identifies off-target sites. The initial bioinformatics algorithms in PROGNOS were validated by predicting 44 of 65 previously confirmed off-target sites, and by uncovering a new off-target site for the extensively studied zinc finger nucleases (ZFNs) targeting C-C chemokine receptor type 5. Using PROGNOS, we rapidly interrogated 128 potential off-target sites for newly designed transcription activator-like effector nucleases containing either Asn-Asn (NN) or Asn-Lys (NK) repeat variable di-residues (RVDs) and 3- and 4-finger ZFNs, and validated 13 bona fide off-target sites for these nucleases by DNA sequencing. The PROGNOS algorithms were further refined by incorporating additional features of nuclease-DNA interactions and the newly confirmed off-target sites into the training set, which increased the percentage of bona fide off-target sites found within the top PROGNOS rankings. By identifying potential off-target sites in silico, PROGNOS allows the selection of more specific target sites and aids the identification of bona fide off-target sites, significantly facilitating the design of engineered nucleases for genome editing applications.
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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.