The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
Open accessAbstract
CRISPR RNA-guided nucleases (RGNs) are widely used genome-editing reagents, but methods to delineate their genome-wide, off-target cleavage activities have been lacking. Here we describe an approach for global detection of DNA double-stranded breaks (DSBs) introduced by RGNs and potentially other nucleases. This method, called genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq), relies on capture of double-stranded oligodeoxynucleotides into DSBs. Application of GUIDE-seq to 13 RGNs in two human cell lines revealed wide variability in RGN off-target activities and unappreciated characteristics of off-target sequences. The majority of identified sites were not detected by existing computational methods or chromatin immunoprecipitation sequencing (ChIP-seq). GUIDE-seq also identified RGN-independent genomic breakpoint 'hotspots'. Finally, GUIDE-seq revealed that truncated guide RNAs exhibit substantially reduced RGN-induced, off-target DSBs. Our experiments define the most rigorous framework for genome-wide identification of RGN off-target effects to date and provide a method for evaluating the safety of these nucleases before clinical use.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source doesn’t support the claim as written.
In the citing paper
“A primary limitation of GUIDE-seq is relevant to the low delivery efficiency of dsODNs into cells, which results in detection of only 30%–50% of all the DSBs (Tsai et al., 2015; Pan et al., 2022).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Tsai et al., 2015
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Off-target profiling of AsCas12a-crRNA+11 genome editing in HEK293/3272-26A>G cells18,42 showed very high specificity, as demonstrated by exclusive editing of the 3272-26A>G CFTR locus, while non-specific cleavages in the second allele, or any other genomic loci, could not be detected (Fig. 2c and Supplementary Fig. 4c).”
From Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing (2019) · cites this paper as [42]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The major barrier of clinical use of CRISPR/Cas9 is its off-target effects [81,82,83].”
From Viral Delivery Systems for CRISPR (2019) · cites this paper as [81]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“While cleavage at sites with perfect complementarity to the protospacer domain of the gRNA typically occurs with highest efficiency, cleavage at sites having one to several bases of mismatch with the gRNA can occur. These undesired cleavage events are called “off-target effects” (OTEs)10, and their existence should be minimized for therapeutic applications of genome editing technologies.”
From A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells (2018) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“The GUIDE-seq procedure10 can be used to empirically identify real off-target sites in cells.”
From A high-fidelity Cas9 mutant delivered as a ribonucleoprotein complex enables efficient gene editing in human hematopoietic stem and progenitor cells (2018) · cites this paper as [10]
The cited source says what the claim attributes to it.
In the citing paper
“GUIDE-seq can detect off-target sites with indel frequencies as low as 0.03% (Tsai et al., 2015).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Tsai et al., 2015
The cited source says what the claim attributes to it.
In the citing paper
“GUIDE-seq is more sensitive than the IDLV method because dsODNs integrate more efficiently and precisely into DSBs, while the integration events of IDLV is low in number and can distribute as far as 500bp away from the actual DSB sites (Tsai et al., 2015; Cromer et al., 2023).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Tsai et al., 2015
The cited source says what the claim attributes to it.
In the citing paper
“However, other publications observed a much lower validation rate (Cencic et al., 2014; Duan et al., 2014; Tsai et al., 2015).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Tsai et al., 2015
The cited source says what the claim attributes to it.
In the citing paper
“These studies indicated that Cas9 could associate with genomic loci without exerting its nuclease function, deposing a major caveat in Cas9 ChIP-Seq-based off-target detection assay.”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Tsai et al., 2015
The cited source says what the claim attributes to it.
In the citing paper
“Interestingly, compared to cell-based methods such as GUIDE-seq (see next section) (Tsai et al., 2015), Extru-seq exhibited much lower false negative rate (2.3% versus 29%) (Kwon et al., 2023).”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Tsai et al., 2015
In the citing paper
“Using the standard Guide-seq protocol, we detected only the Fah target site and one off-target site (defined as Guide-seq off-target site 1, or GOT1) (Supplementary Data Set 1).”
From Adenine base editing in an adult mouse model of tyrosinaemia (2019) · cites this paper as [23]
In the citing paper
“However, silicon methods can only identify part of the off-target cleavage.48”
From CRISPR-Cas9: a new and promising player in gene therapy (2015) · cites this paper as [48]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012) · Science · doi:10.1126/science.1225829 · Cited by 17,116
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133
Development and Applications of CRISPR-Cas9 for Genome Engineering
Hsu, P. D., Lander, E. S., & Zhang, F. (2014) · Cell · doi:10.1016/j.cell.2014.05.010 · Cited by 5,762
DNA targeting specificity of RNA-guided Cas9 nucleases
Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., Li, Y., Fine, E. J., Wu, X., Shalem, O., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2647 · Cited by 4,741
Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity
Ran, F. A., Hsu, P. D., Lin, C.-Y., Gootenberg, J. S., Konermann, S., Trevino, A. E., Scott, D. A., Inoue, A., Matoba, S., Zhang, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.08.021 · Cited by 3,299
High-Frequency off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells
Fu, Y., Foden, J. A., Khayter, C., Maeder, M. L., Reyon, D., Joung, J. K., & Sander, J. D. (2013) · Nature Biotechnology · doi:10.1038/nbt.2623 · Cited by 3,292
Self-citationCRISPR-Cas systems for editing, regulating and targeting genomes
Sander, J. D., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2842 · Cited by 3,153
Self-citationRNA-guided editing of bacterial genomes using CRISPR-Cas systems
Jiang, W., Bikard, D., Cox, D., Zhang, F., & Marraffini, L. A. (2013) · Nature Biotechnology · doi:10.1038/nbt.2508 · Cited by 2,429
Flagged first, then by citations
Cited by
Sorted by citations
Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A., & Liu, D. R. (2016) · Nature · doi:10.1038/nature17946 · Cited by 5,437
Search-and-replace genome editing without double-strand breaks or donor DNA
Anzalone, A. V., Randolph, P. B., Davis, J. R., Sousa, A. A., Koblan, L. W., Levy, J. M., Chen, P. J., Wilson, C., Newby, G. A., Raguram, A., et al. (2019) · Nature · doi:10.1038/s41586-019-1711-4 · Cited by 4,767
Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
Doench, J. G., Fusi, N., Sullender, M., Hegde, M., Vaimberg, E. W., Donovan, K. F., Smith, I., Tothova, Z., Wilen, C., Orchard, R., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3437 · Cited by 4,637
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., & Liu, D. R. (2017) · Nature · doi:10.1038/nature24644 · Cited by 4,184
In vivo genome editing using Staphylococcus aureus Cas9
Ran, F. A., Cong, L., Yan, W. X., Scott, D. A., Gootenberg, J. S., Kriz, A. J., Zetsche, B., Shalem, O., Wu, X., Makarova, K. S., et al. (2015) · Nature · doi:10.1038/nature14299 · Cited by 2,687
High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects
Kleinstiver, B. P., Pattanayak, V., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Zheng, Z., & Joung, J. K. (2016) · Nature · doi:10.1038/nature16526 · Cited by 2,673
Self-citationRationally engineered Cas9 nucleases with improved specificity
Slaymaker, I. M., Gao, L., Zetsche, B., Scott, D. A., Yan, W. X., & Zhang, F. (2016) · Science · doi:10.1126/science.aad5227 · Cited by 2,414
Ma, X., Zhang, Q., Zhu, Q., Liu, W., Chen, Y., Qiu, R., Wang, B., Yang, Z., Li, H., Lin, Y., et al. (2015) · Molecular Plant · doi:10.1016/j.molp.2015.04.007 · Cited by 2,369
Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors
Anzalone, A. V., Koblan, L. W., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0561-9 · Cited by 2,237
Kosicki, M., Tomberg, K., & Bradley, A. (2018) · Nature Biotechnology · doi:10.1038/nbt.4192 · Cited by 1,883
CRISPR-Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis
Gillmore, J. D., Gane, E., Taubel, J., Kao, J., Fontana, M., Maitland, M. L., Seitzer, J., O’Connell, D., Walsh, K. R., Wood, K., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2107454 · Cited by 1,801
Haeussler, M., Schönig, K., Eckert, H., Eschstruth, A., Mianné, J., Renaud, J.-B., Schneider-Maunoury, S., Shkumatava, A., Teboul, L., Kent, J., et al. (2016) · Genome biology · doi:10.1186/s13059-016-1012-2 · Cited by 1,756
Base editing: precision chemistry on the genome and transcriptome of living cells
Rees, H. A., & Liu, D. R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0059-1 · Cited by 1,675
The CRISPR tool kit for genome editing and beyond
Adli, M. (2018) · Nature Communications · doi:10.1038/s41467-018-04252-2 · Cited by 1,545
CRISPResso2 provides accurate and rapid genome editing sequence analysis
Clement, K., Rees, H. A., Canver, M. C., Gehrke, J. M., Farouni, R., Hsu, J. Y., Cole, M. A., Liu, D. R., Joung, J. K., Bauer, D. E., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0032-3 · Cited by 1,656
Self-citationEngineered CRISPR-Cas9 nucleases with altered PAM specificities
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Topkar, V. V., Nguyen, N. T., Zheng, Z., Gonzales, A. P. W., Li, Z., Peterson, R. T., Yeh, J.-R. J., et al. (2015) · Nature · doi:10.1038/nature14592 · Cited by 1,624
Self-citationEvolved Cas9 variants with broad PAM compatibility and high DNA specificity
Hu, J. H., Miller, S. M., Geurts, M. H., Tang, W., Chen, L., Sun, N., Zeina, C. M., Gao, X., Rees, H. A., Lin, Z., et al. (2018) · Nature · doi:10.1038/nature26155 · Cited by 1,552
CRISPR-engineered T cells in patients with refractory cancer
Stadtmauer, E. A., Fraietta, J. A., Davis, M. M., Cohen, A. D., Weber, K. L., Lancaster, E., Mangan, P. A., Kulikovskaya, I., Gupta, M., Chen, F., et al. (2020) · Science · doi:10.1126/science.aba7365 · Cited by 1,478
Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems
Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K. Y., et al. (2016) · Science · doi:10.1126/science.aaf8729 · Cited by 1,349
Therapeutic genome editing: prospects and challenges
Cox, D. B. T., Platt, R. J., & Zhang, F. (2015) · Nature Medicine · doi:10.1038/nm.3793 · Cited by 1,336
Off-target Effects in CRISPR/Cas9-mediated Genome Engineering
Zhang, X.-H., Tee, L. Y., Wang, X.-G., Huang, Q.-S., & Yang, S.-H. (2015) · Molecular Therapy - Nucleic Acids · doi:10.1038/mtna.2015.37 · Cited by 1,273
CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response
Haapaniemi, E., Botla, S., Persson, J., Schmierer, B., & Taipale, J. (2018) · Nature Medicine · doi:10.1038/s41591-018-0049-z · Cited by 1,264
High-throughput functional genomics using CRISPR-Cas9
Shalem, O., Sanjana, N. E., & Zhang, F. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3899 · Cited by 1,233
Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants
Walton, R. T., Christie, K. A., Whittaker, M. N., & Kleinstiver, B. P. (2020) · Science · doi:10.1126/science.aba8853 · Cited by 1,233
Gene therapy returns to centre stage
Naldini, L. (2015) · Nature · doi:10.1038/nature15818 · Cited by 1,184
Enhanced proofreading governs CRISPR-Cas9 targeting accuracy
Chen, J. S., Dagdas, Y. S., Kleinstiver, B. P., Welch, M. M., Sousa, A. A., Harrington, L. B., Sternberg, S. H., Joung, J. K., Yildiz, A., & Doudna, J. A. (2017) · Nature · doi:10.1038/nature24268 · Cited by 1,168
Self-citationEngineered CRISPR-Cas9 nuclease with expanded targeting space
Nishimasu, H., Shi, X., Ishiguro, S., Gao, L., Hirano, S., Okazaki, S., Noda, T., Abudayyeh, O. O., Gootenberg, J. S., Mori, H., et al. (2018) · Science · doi:10.1126/science.aas9129 · Cited by 1,100
Richter, M. F., Zhao, K. T., Eton, E., Lapinaite, A., Newby, G. A., Thuronyi, B. W., Wilson, C., Koblan, L. W., Zeng, J., Bauer, D. E., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0453-z · Cited by 1,020
CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes
Komor, A. C., Badran, A. H., & Liu, D. R. (2016) · Cell · doi:10.1016/j.cell.2016.10.044 · Cited by 1,037
Digenome-seq: Genome-wide profiling of CRISPR-cas9 off-target effects in human cells
Kim, D., Bae, S., Park, J., Kim, E., Kim, S., Yu, H. R., Hwang, J., Kim, J.-I., & Kim, J.-S. (2015) · Nature Methods · doi:10.1038/nmeth.3284 · Cited by 992
p53 inhibits CRISPR–Cas9 engineering in human pluripotent stem cells
Ihry, R. J., Worringer, K. A., Salick, M. R., Frias, E., Ho, D., Theriault, K., Kommineni, S., Chen, J., Sondey, M., Ye, C., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0050-6 · Cited by 978
Long, C., Amoasii, L., Mireault, A. A., McAnally, J., Li, H. Z., Sanchez‐Ortiz, E., Bhattacharyya, S., Shelton, J. M., Bassel‐Duby, R., & Olson, E. N. (2015) · Science · doi:10.1126/science.aad5725 · Cited by 973
CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
Labun, K., Montague, T. G., Gagnon, J. A., Thyme, S. B., & Valen, E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw398 · Cited by 954
Yin, H., Song, C.-Q., Dorkin, J. R., Zhu, L. J., Li, Y., Wu, Q., Park, A., Yang, J., Suresh, S., Bizhanova, A., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3471 · Cited by 876
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
Dominguez, A. A., Lim, W. A., & Qi, L. S. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.2 · Cited by 832
CIRCLE-Seq: A highly sensitive in vitro screen for genome-wide CRISPR-cas9 nuclease off-targets
Tsai, S. Q., Nguyen, N. T., Malagon-Lopez, J., Topkar, V. V., Aryee, M. J., & Joung, J. K. (2017) · Nature Methods · doi:10.1038/nmeth.4278 · Cited by 814
Self-citationTools for translation: non-viral materials for therapeutic mRNA delivery
Hajj, K. A., & Whitehead, K. A. (2017) · Nature Reviews Materials · doi:10.1038/natrevmats.2017.56 · Cited by 799
Vakulskas, C. A., Dever, D. P., Rettig, G. R., Turk, R., Jacobi, A. M., Collingwood, M. A., Bode, N. M., McNeill, M. S., Yan, S., Camarena, J., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0137-0 · Cited by 782
Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos
Zuo, E., Sun, Y., Wei, W., Yuan, T., Ying, W., Sun, H., Yuan, L., Steinmetz, L. M., Li, Y., & Yang, H. (2019) · Science · doi:10.1126/science.aav9973 · Cited by 782
Natural killer cells in antitumour adoptive cell immunotherapy
Laskowski, T. J., Biederstädt, A., & Rezvani, K. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00491-0 · Cited by 810
Whole-organism lineage tracing by combinatorial and cumulative genome editing
McKenna, A., Findlay, G. M., Gagnon, J. A., Horwitz, M. S., Schier, A. F., & Shendure, J. (2016) · Science · doi:10.1126/science.aaf7907 · Cited by 766
Rupp, L. J., Schumann, K., Roybal, K. T., Gate, R. E., Ye, C. J., Lim, W. A., & Marson, A. (2017) · Scientific Reports · doi:10.1038/s41598-017-00462-8 · Cited by 757
Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells
Kim, D., Kim, J., Hur, J. K., Been, K. W., Yoon, S.-H., & Kim, J.-S. (2016) · Nature Biotechnology · doi:10.1038/nbt.3609 · Cited by 731
Engineered pegRNAs improve prime editing efficiency
Nelson, J. W., Randolph, P. B., Shen, S. P., Everette, K. A., Chen, P. J., Anzalone, A. V., An, M., Newby, G. A., Chen, J. C., Hsu, A., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01039-7 · Cited by 727
Genome-editing Technologies for Gene and Cell Therapy
Maeder, M. L., & Gersbach, C. A. (2016) · Molecular Therapy · doi:10.1038/mt.2016.10 · Cited by 736
Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10
Maeder, M. L., Stefanidakis, M., Wilson, C. J., Baral, R., Barrera, L. A., Bounoutas, G. S., Bumcrot, D., Chao, H., Ciulla, D. M., DaSilva, J. A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-018-0327-9 · Cited by 707
Kleinstiver, B. P., Sousa, A. A., Walton, R. T., Tak, Y. E., Hsu, J. Y., Clement, K., Welch, M. M., Horng, J. E., Malagon-Lopez, J., Scarfò, I., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0011-0 · Cited by 698
Self-citationGenome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells
Kleinstiver, B. P., Tsai, S. Q., Prew, M. S., Nguyen, N. T., Welch, M. M., Lopez, J. M., McCaw, Z. R., Aryee, M. J., & Joung, J. K. (2016) · Nature Biotechnology · doi:10.1038/nbt.3620 · Cited by 670
Self-citationDeepCRISPR: Optimized CRISPR guide RNA design by deep learning
Chuai, G., Ma, H., Yan, J., Chen, M., Hong, N., Xue, D., Zhou, C., Zhu, C., Chen, K., Duan, B., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1459-4 · Cited by 641
Conformational control of DNA target cleavage by CRISPR–Cas9
Sternberg, S. H., LaFrance, B., Kaplan, M., & Doudna, J. A. (2015) · Nature · doi:10.1038/nature15544 · Cited by 627
Off-target effects in CRISPR/Cas9 gene editing
Guo, C., Ma, X., Gao, F., & Guo, Y. (2023) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1143157 · Cited by 704
“The integrated dsODNs provide templates for targeted PCR amplification and sequencing of the tagged DNA fragments (Tsai et al., 2015; Malinin et al., 2021; Yaish et al., 2022) (Figure 1B).”
BackgroundMethodInfluentialSequence determinants of improved CRISPR sgRNA design
Xu, H., Xiao, T., Chen, C.-H., Li, W., Meyer, C. A., Wu, Q., Wu, D., Cong, L., Zhang, F., Liu, J. S., et al. (2015) · Genome Research · doi:10.1101/gr.191452.115 · Cited by 625
Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition
Kleinstiver, B. P., Prew, M. S., Tsai, S. Q., Nguyen, N. T., Topkar, V. V., Zheng, Z., & Joung, J. K. (2015) · Nature Biotechnology · doi:10.1038/nbt.3404 · Cited by 611
Self-citationPast, present, and future of CRISPR genome editing technologies
Pacesa, M., Pelea, O., & Jinek, M. (2024) · Cell · doi:10.1016/j.cell.2024.01.042 · Cited by 609
Combination Immunotherapy with CAR T Cells and Checkpoint Blockade for the Treatment of Solid Tumors
Grosser, R., Cherkassky, L., Chintala, N., & Adusumilli, P. S. (2019) · Cancer Cell · doi:10.1016/j.ccell.2019.09.006 · Cited by 603
Delivery technologies for genome editing
Yin, H., Kauffman, K. J., & Anderson, D. G. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.280 · Cited by 597
CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells
Kurt, I. C., Zhou, R., Iyer, S., Garcia, S. P., Miller, B. R., Langner, L. M., Grünewald, J., & Joung, J. K. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0609-x · Cited by 573
Self-citationThe CRISPR-Cas immune system: Biology, mechanisms and applications
Rath, D., Amlinger, L., Rath, A., & Lundgren, M. (2015) · Biochimie · doi:10.1016/j.biochi.2015.03.025 · Cited by 471
Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Aguirre, A. J., Meyers, R. M., Weir, B. A., Vázquez, F., Zhang, C., Ben‐David, U., Cook, A., Ha, G., Harrington, W. F., Doshi, M. B., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0154 · Cited by 580
Wang, H.-X., Li, M., Lee, C. M., Chakraborty, S., Kim, H.-W., Bao, G., & Leong, K. W. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00799 · Cited by 560
A dual AAV system enables the Cas9-mediated correction of a metabolic liver disease in newborn mice
Yang, Y., Wang, L., Bell, P., McMenamin, D., He, Z., White, J., Yu, H., Xu, C., Morizono, H., Musunuru, K., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3469 · Cited by 556
“More extensive characterization of these potential toxicities is necessary before clinical translation can be considered 24,25 , although, in animals treated as newborns, we could not detect indels of likely off-target sites at the level of sensitivity achieved by deep sequencing.”
Multiplexed CRISPR technologies for gene editing and transcriptional regulation
McCarty, N. S., Graham, A. E., Studená, L., & Ledesma‐Amaro, R. (2020) · Nature Communications · doi:10.1038/s41467-020-15053-x · Cited by 567
Lü, Y., Xue, J., Deng, T., Zhou, X., Yu, K., Deng, L., Huang, M., Yi, X., Liang, M., Wang, Y., et al. (2020) · Nature Medicine · doi:10.1038/s41591-020-0840-5 · Cited by 553
Treatment of autosomal dominant hearing loss by in vivo delivery of genome editing agents
Gao, X., Tao, Y., Lamas, V., Huang, M., Yeh, W.-H., Pan, B., Hu, Y.-J., Hu, J. H., Thompson, D. B., Shu, Y., et al. (2018) · Nature · doi:10.1038/nature25164 · Cited by 536
CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors
Wang, D., Zhang, F., & Gao, G. (2020) · Cell · doi:10.1016/j.cell.2020.03.023 · Cited by 539
Directed evolution of adenine base editors with increased activity and therapeutic application
Gaudelli, N. M., Lam, D. K., Rees, H. A., Solá-Esteves, N. M., Barrera, L. A., Born, D. A., Edwards, A., Gehrke, J. M., Lee, S., Liquori, A., et al. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0491-6 · Cited by 533
Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR
Boettcher, M., & McManus, M. T. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.028 · Cited by 539
Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases
Tsai, S. Q., & Joung, J. K. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.28 · Cited by 523
Self-citationInduced Pluripotent Stem Cells Meet Genome Editing
Hockemeyer, D., & Jaenisch, R. (2016) · Cell Stem Cell · doi:10.1016/j.stem.2016.04.013 · Cited by 499
“Moreover, the GUIDE-Seq. protocol was also used to engineer CRISPR-Cas9 nucleases with altered PAM Cell Stem Cell.”
BackgroundMethodStructure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing
Yin, H., Song, C.-Q., Suresh, S., Wu, Q., Walsh, S., Rhym, L. H., Mintzer, E., Bolukbasi, M. F., Zhu, L. J., Kauffman, K., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.4005 · Cited by 499
A highly specific SpCas9 variant is identified by in vivo screening in yeast
Casini, A., Olivieri, M., Petris, G., Montagna, C., Reginato, G., Maule, G., Lorenzin, F., Prandi, D., Romanel, A., Demichelis, F., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4066 · Cited by 493
Cheating evolution: engineering gene drives to manipulate the fate of wild populations
Champer, J., Buchman, A. B., & Akbari, O. S. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.34 · Cited by 492
Mapping the genomic landscape of CRISPR-Cas9 cleavage
Cameron, P., Fuller, C. K., Donohoue, P. D., Jones, B. N., Thompson, M. S., Carter, M. M., Gradia, S., Vidal, B., Garner, E., Slorach, E. M., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4284 · Cited by 443
Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors
Doman, J. L., Raguram, A., Newby, G. A., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0414-6 · Cited by 473
CD7-edited T cells expressing a CD7-specific CAR for the therapy of T-cell malignancies
Gomes‐Silva, D., Srinivasan, M., Sharma, S., Lee, C. M., Wagner, D. L., Davis, T., Rouce, R. H., Bao, G., Brenner, M. K., & Mamonkin, M. (2017) · Blood · doi:10.1182/blood-2017-01-761320 · Cited by 477
Latest Developed Strategies to Minimize the Off-Target Effects in CRISPR-Cas-Mediated Genome Editing
Naeem, M., Majeed, S., Hoque, M. Z., & Ahmad, I. (2020) · Cells · doi:10.3390/cells9071608 · Cited by 457
Am I ready for CRISPR? A user's guide to genetic screens
Doench, J. G. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.97 · Cited by 452
Cornerstones of CRISPR–Cas in drug discovery and therapy
Fellmann, C., Gowen, B. G., Lin, P., Doudna, J. A., & Corn, J. E. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.238 · Cited by 452
CRISPR in cancer biology and therapy
Katti, A., Diaz, B. J., Caragine, C. M., Sanjana, N. E., & Dow, L. E. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00441-w · Cited by 457
Progress and prospects in plant genome editing
Yin, K., Gao, C., & Qiu, J. (2017) · Nature Plants · doi:10.1038/nplants.2017.107 · Cited by 445
Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq
Wienert, B., Wyman, S. K., Richardson, C. D., Yeh, C. D., Akcakaya, P., Porritt, M. J., Morlock, M., Vu, J. T., Kazane, K. R., Watry, H. L., et al. (2019) · Science · doi:10.1126/science.aav9023 · Cited by 434
An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities
Gehrke, J. M., Cervantes, O., Clement, K., Wu, Y., Zeng, J., Bauer, D. E., Pinello, L., & Joung, J. K. (2018) · Nature Biotechnology · doi:10.1038/nbt.4199 · Cited by 439
Self-citationHigh levels of AAV vector integration into CRISPR-induced DNA breaks
Hanlon, K. S., Kleinstiver, B. P., Garcia, S. P., Zaborowski, M. P., Volak, A., Spirig, S. E., Muller, A., Sousa, A. A., Tsai, S. Q., Bengtsson, N. E., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12449-2 · Cited by 431
Self-citationRees, H. A., Komor, A. C., Yeh, W.-H., Caetano-Lopes, J., Warman, M., Edge, A. S. B., & Liu, D. R. (2017) · Nature Communications · doi:10.1038/ncomms15790 · Cited by 412
Small molecule–triggered Cas9 protein with improved genome-editing specificity
Davis, K. M., Pattanayak, V., Thompson, D. B., Zuris, J. A., & Liu, D. R. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1793 · Cited by 427
Patient-Specific In Vivo Gene Editing to Treat a Rare Genetic Disease
Musunuru, K., Grandinette, S. A., Wang, X., Hudson, T. R., Briseno, K., Berry, A. M., Hacker, J. L., Hsu, A., Silverstein, R. A., Hille, L. T., et al. (2025) · New England Journal of Medicine · doi:10.1056/nejmoa2504747 · Cited by 409
Gene Editing and Crop Improvement Using CRISPR-Cas9 System
Arora, L., & Narula, A. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.01932 · Cited by 412
Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach
Chari, R., Mali, P., Moosburner, M., & Church, G. M. (2015) · Nature Methods · doi:10.1038/nmeth.3473 · Cited by 404
Manghwar, H., Li, B., Ding, X., Hussain, A., Lindsey, K., Zhang, X., & Jin, S. (2020) · Advanced Science · doi:10.1002/advs.201902312 · Cited by 347
An “off-the-shelf” fratricide-resistant CAR-T for the treatment of T cell hematologic malignancies
Cooper, M. L., Choi, J., Staser, K. W., Ritchey, J., Devenport, J. M., Eckardt, K., Rettig, M. P., Wang, B., Eissenberg, L. G., Ghobadi, A., et al. (2018) · Leukemia · doi:10.1038/s41375-018-0065-5 · Cited by 398
Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes
Morgens, D. W., Deans, R. M., Li, A., & Bassik, M. C. (2016) · Nature Biotechnology · doi:10.1038/nbt.3567 · Cited by 398
In vivo high-throughput profiling of CRISPR-Cpf1 activity
Kim, H. K., Song, M., Lee, J., Menon, A. V., Jung, S., Kang, Y.-M., Choi, J. W., Woo, E., Koh, H. C., Nam, J.-W., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4104 · Cited by 383
Pan, C., Ye, L., Li, Q., Liu, X., He, Y., Wang, J., Chen, L., & Lu, G. (2016) · Scientific Reports · doi:10.1038/srep24765 · Cited by 391
Non-viral, specifically targeted CAR-T cells achieve high safety and efficacy in B-NHL
Zhang, J., Hu, Y., Yang, J., Li, W., Zhang, M., Wang, Q., Zhang, L., Wei, G., Tian, Y., Zhao, K., et al. (2022) · Nature · doi:10.1038/s41586-022-05140-y · Cited by 397
WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system
Wong, N. W., Liu, W., & Wang, X. (2015) · Genome biology · doi:10.1186/s13059-015-0784-0 · Cited by 383
CRISPRi and CRISPRa Screens in Mammalian Cells for Precision Biology and Medicine
Kampmann, M. (2017) · ACS Chemical Biology · doi:10.1021/acschembio.7b00657 · Cited by 387
BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks
Yan, W. X., Mirzazadeh, R., Garnerone, S., Scott, D., Schneider, M. W., Kallas, T., Custodio, J., Wernersson, E., Li, Y., Gao, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms15058 · Cited by 369
Developmental barcoding of whole mouse via homing CRISPR
Kalhor, R., Kalhor, K., Mejia, L., Leeper, K., Graveline, A., Mali, P., & Church, G. M. (2018) · Science · doi:10.1126/science.aat9804 · Cited by 363
Engineering of CRISPR-Cas12b for human genome editing
Strecker, J., Jones, S., Koopal, B., Schmid-Burgk, J. L., Zetsche, B., Gao, L. A., Makarova, K. S., Koonin, E. V., & Zhang, F. (2019) · Nature Communications · doi:10.1038/s41467-018-08224-4 · Cited by 365
Muñoz, D. M., Cassiani, P. J., Li, L., Billy, É., Korn, J. M., Jones, M. D., Golji, J., Ruddy, D. A., Yu, K., McAllister, G., et al. (2016) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0178 · Cited by 356
Metadata
- Authors
- Tsai, S. Q., Zheng, Z., Nguyen, N. T., Liebers, M., Topkar, V. V., Thapar, V., Wyvekens, N., Khayter, C., Iafrate, A. J., Le, L. P., Aryee, M. J., & Joung, J. K.
- Affiliations
- Harvard University (US)
- Massachusetts General Hospital (US)
- Corresponding author
- Tsai, Shengdar Q
- Joung, J Keith
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2014-12-16
- Volume
- 33
- Issue
- 2
- Pages
- 187-197
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC4320685
- OpenAlex
- W2003797386
- Cited by
- 2,268
- References
- 39
- Citations by year
- 2026: 189 · 2025: 211 · 2024: 196 · 2023: 191 · 2022: 208 · 2021: 211 · 2020: 231 · 2019: 186 · 2018: 187 · 2017: 177 · 2016: 172 · 2015: 105 · 2014: 1
- FWCI
- 62.14
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- National Institute of General Medical Sciences (DP1GM105378, R01GM088040, F32GM105189)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01AR063070)
- National Center for Chronic Disease Prevention and Health Promotion (DP1 GM105378)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- GUIDE-seq, CRISPR-Cas nucleases, off-target cleavage, DNA double-strand breaks, genome-wide characterization, genome editing safety
- MeSH terms
- RNA, Guide, CRISPR-Cas Systems, Cell Line, Humans, Oligodeoxyribonucleotides, Genome, Human, RNA Editing, DNA Breaks, Double-Stranded, High-Throughput Nucleotide Sequencing, CRISPR-Cas Systems
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
