ArticleGenome research2016
Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers, 2 of them syntheses that pooled it.
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
124 citing papers in PubMed, 2 syntheses or guidelines pooled it, 208 citations in OpenAlex.
- Transitioning from wet lab to artificial intelligence: a systematic review of AI predictors in CRISPR.Journal of translational medicine · 2025Pooled it
- An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools.RNA biology · 2020Pooled it
- Trial
- CRISPR-enhanced microalgae for carbon sequestration and carotenoid production: opportunities and fundamental constraints.Bioresources and bioprocessing · 2026Review
- The future of pediatric gene therapy: CRISPR-Cas9, AI, and personalized medicine.Pediatric research · 2026Review
- DeepCas12a: a hybrid deep learning framework for accurate AsCas12a efficiency prediction from sequence and epigenetic information.BMC genomics · 2026Article
- High-fidelity genome and prime editing enabled by the AI-designed openCRISPR-1.Genome medicine · 2026Article
- Nickase NmCas9 unsilences paternal Ube3a in a mouse model of Angelman syndrome without causing AAV vector integration.Scientific reports · 2026Article
- Multilevel characterization of genome editor nuclease activity with BreakTag.Nature protocols · 2026Review
- Avenues of genome editing for color trait improvement in ornamental fishes: current status and future perspectives.Transgenic research · 2025Review
- Identifying optimal conditions for precise knock-in of exogenous DNA into the zebrafish genome.Development (Cambridge, England) · 2025Article
- Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing.Nature biotechnology · 2025Article
- Gene Editing for Enhanced Swine Production: Current Advances and Prospects.Animals : an open access journal from MDPI · 2025Review
- CRISPR and gene editing technologies for bleeding disorders.Therapeutic advances in hematology · 2025Review
- AI-driven advances in plant biotechnology: sharpening the edge of plant tissue culture and genome editing.Frontiers in plant science · 2025Review
- Large DNA deletions occur during DNA repair at 20-fold lower frequency for base editors and prime editors than for Cas9 nucleases.Nature biomedical engineering · 2025Article
- CRISPR-based editing strategies to rectifyMolecular therapy. Nucleic acids · 2024Article
- Engineering of Cas12a nuclease variants with enhanced genome-editing specificity.PLoS biology · 2024Article
- CRISPR-DIPOFF: an interpretable deep learning approach for CRISPR Cas-9 off-target prediction.Briefings in bioinformatics · 2024Article
- Breaking genetic shackles: The advance of base editing in genetic disorder treatment.Frontiers in pharmacology · 2024Review
64 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
No grant is acknowledged in the PubMed record.
Abstract
We present multiplex Digenome-seq to profile genome-wide specificities of up to 11 CRISPR-Cas9 nucleases simultaneously, saving time and reducing cost. Cell-free human genomic DNA was digested using multiple sgRNAs combined with the Cas9 protein and then subjected to whole-genome sequencing. In vitro cleavage patterns, characteristic of on- and off-target sites, were computationally identified across the genome using a new DNA cleavage scoring system. We found that many false-positive, bulge-type off-target sites were cleaved by sgRNAs transcribed from an oligonucleotide duplex but not by those transcribed from a plasmid template. Multiplex Digenome-seq captured many bona fide off-target sites, missed by other genome-wide methods, at which indels were induced at frequencies <0.1%. After analyzing 964 sites cleaved in vitro by these sgRNAs and measuring indel frequencies at hundreds of off-target sites in cells, we propose a guideline for the choice of target sites for minimizing CRISPR-Cas9 off-target effects in the human genome.
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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.