ArticleNucleic acids research2023
Detection of unintended on-target effects in CRISPR genome editing by DNA donors carrying diagnostic substitutions.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- Off-target detection of CRISPR-Cas9 nucleaseSynthetic biology (Oxford, England) · 2026Article
- Search-and-remove genome editing allows selection of cells by DNA sequence.Nature communications · 2025Article
- Robust prediction of synthetic gRNA activity and cryptic DNA repair by disentangling cellular CRISPR cleavage outcomes.Nature communications · 2025Article
- DCHS1 Modulates Forebrain Proportions in Modern Humans via a Glycosylation Change.bioRxiv : the preprint server for biology · 2025Article
- AI-driven advances in plant biotechnology: sharpening the edge of plant tissue culture and genome editing.Frontiers in plant science · 2025Review
- AAV vector-derived elements integrate into Cas9-generated double-strand breaks and disrupt gene transcription.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- Targeted Gene Insertion: The Cutting Edge of CRISPR Drug Development with Hemophilia as a Highlight.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2024Review
- Efficient multi-allelic genome editing via CRISPR-Cas9 ribonucleoprotein-based delivery toFrontiers in plant science · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CRISPR nucleases can introduce double-stranded DNA breaks in genomes at positions specified by guide RNAs. When repaired by the cell, this may result in the introduction of insertions and deletions or nucleotide substitutions provided by exogenous DNA donors. However, cellular repair can also result in unintended on-target effects, primarily larger deletions and loss of heterozygosity due to gene conversion. Here we present a strategy that allows easy and reliable detection of unintended on-target effects as well as the generation of control cells that carry wild-type alleles but have demonstratively undergone genome editing at the target site. Our 'sequence-ascertained favorable editing' (SAFE) donor approach relies on the use of DNA donor mixtures containing the desired nucleotide substitutions or the wild-type alleles together with combinations of additional 'diagnostic' substitutions unlikely to have any effects. Sequencing of the target sites then results in that two different sequences are seen when both chromosomes are edited with 'SAFE' donors containing different sets of substitutions, while a single sequence indicates unintended effects such as deletions or gene conversion. We analyzed more than 850 human embryonic stem cell clones edited with 'SAFE' donors and detect all copy number changes and almost all clones with gene conversion.
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Registered trials
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