ArticleMolecular therapy : the journal of the American Society of Gene Therapy2021
Rational Selection of CRISPR-Cas9 Guide RNAs for Homology-Directed Genome Editing.
Article in Molecular therapy : the journal of the American Society of Gene Therapy, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 45 citations in OpenAlex.
- In vivo systematic detection of the outcomes of CRISPR-Cas9-mediated DNA repair in skeletal muscle stem cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- Engineering B cells to express fully customizable antibodies with enhanced Fc functions.Nature communications · 2026Article
- In vivo production of an anti-HIV antibody in mice by non-viral gene knockin in primate hematopoietic stem and progenitor cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- DNA-PKcs inhibitor AZD7648 reveals sgRNA cross-contaminants and enhanced sensitivity of genome engineering off-target activity in HSPCs.Nucleic acids research · 2026Article
- Ultra-large targeted DNA integrations in primary human cells.bioRxiv : the preprint server for biology · 2026Article
- Heavy-chain immunoglobulin locus editing in rhesus macaque B cells to confer antibody production.Molecular therapy. Methods & clinical development · 2025Article
- Efficient non-viral immune cell engineering using circular single-stranded DNA-mediated genomic integration.Nature biotechnology · 2025Article
- Engineering B cells to Express Fully Customizable Antibodies with Enhanced Fc Functions.Research square · 2025Article
- Refined DNA repair manipulation enables a universal knock-in strategy in mouse embryos.Nature communications · 2025Article
- Gene editing of CD3 epsilon to redirect regulatory T cells for adoptive T cell transfer.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Reprogramming human B cells with custom heavy-chain antibodies.Nature biomedical engineering · 2024Article
- DNA-PK inhibition enhances gene editing efficiency in HSPCs for CRISPR-based treatment of X-linked hyper IgM syndrome.Molecular therapy. Methods & clinical development · 2024Article
- High-efficiency transgene integration by homology-directed repair in human primary cells using DNA-PKcs inhibition.Nature biotechnology · 2024Article
- Impact of CRISPR/HDR editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques.Cell stem cell · 2024Article
- Cas9 RNP Physiochemical Analysis for Enhanced CRISPR-AuNP Assembly and Function.bioRxiv : the preprint server for biology · 2024Article
- Functional screening in human HSPCs identifies optimized protein-based enhancers of Homology Directed Repair.Nature communications · 2024Article
- Efficient and sustainedMolecular therapy. Methods & clinical development · 2024Article
- Preclinical evaluation of CRISPR-based therapies for Noonan syndrome caused by deep-intronicMolecular therapy. Nucleic acids · 2024Article
- Increasing Gene Editing Efficiency via CRISPR/Cas9- or Cas12a-Mediated Knock-In in Primary Human T Cells.Biomedicines · 2024Review
- Efficient high-precision homology-directed repair-dependent genome editing by HDRobust.Nature methods · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Homology-directed repair (HDR) of a DNA break allows copying of genetic material from an exogenous DNA template and is frequently exploited in CRISPR-Cas9 genome editing. However, HDR is in competition with other DNA repair pathways, including non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ), and the efficiency of HDR outcomes is not predictable. Consequently, to optimize HDR editing, panels of CRISPR-Cas9 guide RNAs (gRNAs) and matched homology templates must be evaluated. We report here that CRISPR-Cas9 indel signatures can instead be used to identify gRNAs that maximize HDR outcomes. Specifically, we show that the frequency of deletions resulting from MMEJ repair, characterized as deletions greater than or equal to 3 bp, better predicts HDR frequency than consideration of total indel frequency. We further demonstrate that tools that predict gRNA indel signatures can be repurposed to identify gRNAs to promote HDR. Finally, by comparing indels generated by S. aureus and S. pyogenes Cas9 targeted to the same site, we add to the growing body of data that the targeted DNA sequence is a major factor governing genome editing outcomes.
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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.