Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq
Open accessAbstract
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.
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
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 specificity of Cas9 activity can be enhanced by extending or truncating sgRNAs.
“accumulative evidence showed that the specificity of Cas9 activity can be enhanced by extending or truncating sgRNAs”
From Off-target effects in CRISPR/Cas9 gene editing (2023) · cites this paper as Kim et al., 2016
The Results (Validation of off-target sites in cells; page unavailable) report that sgRNAs extended with two 5′ guanines were up to 598-fold more specific than conventional sgRNAs. The Discussion (page unavailable) says truncated sgRNAs can also be highly specific, but only when they target rare, sufficiently unique 17-nt sites; it does not establish that truncation itself enhances specificity relative to full-length sgRNAs. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
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 · see citing works
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339 · see citing works
RNA-Guided Human Genome Engineering via Cas9
Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., & Church, G. M. (2013) · Science · doi:10.1126/science.1232033 · Cited by 9,210 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937 · see citing works
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 · see citing works
RNA-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 · see citing works
Bae, S., Park, J., & Kim, J.-S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu048 · Cited by 2,339 · see citing works
Self-citationGUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
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., et al. (2015) · Nature Biotechnology · doi:10.1038/nbt.3117 · Cited by 2,268 · see citing works
RNA-programmed genome editing in human cells
Jinek, M., East, A., Cheng, A., Lin, S., Ma, E., & Doudna, J. (2013) · eLife · doi:10.7554/elife.00471 · Cited by 2,098 · see citing works
Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2808 · Cited by 1,993 · cited 2× · see citing works
“2015), and modified guide RNAs(Cho et al. 2014; Fu et al. 2014).”
BackgroundTargeted genome engineering in human cells with the Cas9 RNA-guided endonuclease
Cho, S. W., Kim, S., Kim, J. M., & Kim, J.-S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2507 · Cited by 1,863 · see citing works
Self-citationKim, S., Kim, D., Cho, S. W., Kim, J., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.171322.113 · Cited by 1,856 · see citing works
Self-citationMali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L., & Church, G. M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2675 · Cited by 1,752 · cited 3× · see citing works
“To minimize or avoid RGEN off-target effects, we and others have proposed various methods, which include dimeric Cas9 systems (paired Cas9 nickases [Mali et al. 2013a; Ran et al. 2013; Cho et al. 2014] and dCas9-FokI [Guilinger et al. 2014; Tsai et al. 2014]), delivery of RGEN ribonucleoproteins…”
BackgroundMethodPattanayak, V., Lin, S., Guilinger, J. P., Ma, E., Doudna, J. A., & Liu, D. R. (2013) · Nature Biotechnology · doi:10.1038/nbt.2673 · Cited by 1,487 · cited 3× · see citing works
“www.genome.org 10-nt “seed” region (Jinek et al. 2012; Cong et al. 2013; Pattanayak et al. 2013).”
BackgroundZuris, J. A., Thompson, D. B., Shu, Y., Guilinger, J. P., Bessen, J. L., Hu, J. H., Maeder, M. L., Joung, J. K., Chen, Z.-Y., & Liu, D. R. (2015) · Nature Biotechnology · doi:10.1038/nbt.3081 · Cited by 1,460 · see citing works
Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
Cho, S. W., Kim, S., Kim, Y., Kweon, J., Kim, H. S., Bae, S., & Kim, J.-S. (2014) · Genome Research · doi:10.1101/gr.162339.113 · Cited by 1,356 · see citing works
Self-citationEbola virus entry requires the cholesterol transporter Niemann–Pick C1
Carette, J. E., Raaben, M., Wong, A., Herbert, A. S., Obernosterer, G., Mulherkar, N., Kuehne, A. I., Kranzusch, P. J., Griffin, A. M., Ruthel, G. T., et al. (2011) · Nature · doi:10.1038/nature10348 · Cited by 1,309 · see citing works
A guide to genome engineering with programmable nucleases
Kim, S., & Kim, J. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3686 · Cited by 1,162 · see citing works
Self-citationCunningham, F., Amode, M. R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1010 · Cited by 1,115 · see citing works
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 · see citing works
Self-citationDimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing
Tsai, S. Q., Wyvekens, N., Khayter, C., Foden, J. A., Thapar, V., Reyon, D., Goodwin, M. J., Aryee, M. J., & Joung, J. K. (2014) · Nature Biotechnology · doi:10.1038/nbt.2908 · Cited by 952 · see citing works
Guilinger, J. P., Thompson, D. B., & Liu, D. R. (2014) · Nature Biotechnology · doi:10.1038/nbt.2909 · Cited by 836 · see citing works
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Kuscu, C., Arslan, S., Singh, R., Thorpe, J., & Adli, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2916 · Cited by 777 · see citing works
Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
Frock, R. L., Hu, J., Meyers, R. M., Ho, Y.-J., Kii, E., & Alt, F. W. (2015) · Nature Biotechnology · doi:10.1038/nbt.3101 · Cited by 673 · see citing works
Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA
Ramakrishna, S., Kwaku Dad, A.-B., Beloor, J., Gopalappa, R., Lee, S.-K., & Kim, H. (2014) · Genome Research · doi:10.1101/gr.171264.113 · Cited by 655 · see citing works
Self-citationLin, Y., Cradick, T. J., Brown, M. T., Deshmukh, H., Ranjan, P., Sarode, N., Wile, B. M., Vertino, P. M., Stewart, F. J., & Bao, G. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku402 · Cited by 634 · see citing works
CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity
Cradick, T. J., Fine, E. J., Antico, C. J., & Bao, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt714 · Cited by 590 · see citing works
Chiarle, R., Zhang, Y., Frock, R. L., Lewis, S. M., Molinié, B., Ho, Y.-J., Myers, D. R., Choi, V. W., Compagno, M., Malkin, D. J., et al. (2011) · Cell · doi:10.1016/j.cell.2011.07.049 · Cited by 475 · see citing works
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing
Crosetto, N., Mitra, A., Silva, M. J., Bienko, M., Dojer, N., Wang, Q., Karaca, E., Chiarle, R., Skrzypczak, M., Ginalski, K., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2408 · Cited by 465 · see citing works
Wang, X., Wang, Y., Wu, X., Wang, J., Wang, Y., Qiu, Z., Chang, T., Huang, H., Lin, R.-J., & Yee, J.-K. (2015) · Nature Biotechnology · doi:10.1038/nbt.3127 · Cited by 442 · see citing works
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms
Raczy, C., Petrovski, R., Saunders, C. T., Chorny, I., Kruglyak, S., Margulies, E. H., Chuang, H., Källberg, M., Kumar, S. A., Liao, A. K., et al. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt314 · Cited by 333 · see citing works
Cho, S. W., Lee, J., Carroll, D., Kim, J., & Lee, J. (2013) · Genetics · doi:10.1534/genetics.113.155853 · Cited by 248 · see citing works
Self-citationStarcode: sequence clustering based on all-pairs search
Zorita, E. V., Cuscó, P., & Filion, G. J. P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv053 · Cited by 241 · see citing works
Mapping the precision of genome editing
Gabriel, R., Kalle, C. V., & Schmidt, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3142 · Cited by 40 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
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 · see citing works
Correction of a pathogenic gene mutation in human embryos
Ma, H., Marti-Gutierrez, N., Park, S.-W., Wu, J., Lee, Y., Suzuki, K., Koski, A., Ji, D., Hayama, T., Ahmed, R., et al. (2017) · Nature · doi:10.1038/nature23305 · Cited by 969 · see citing works
Self-citationGenome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes
Svitashev, S. K., Schwartz, C., Lenderts, B., Young, J. K., & Cigan, A. M. (2016) · Nature Communications · doi:10.1038/ncomms13274 · Cited by 826 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 625 · see citing works
“Apart from the impact of sgRNA sequences, accumulative evidence showed that the specificity of Cas9 activity can be enhanced by extending or truncating sgRNAs (Cho et al., 2014; Fu et al., 2014; Kim et al., 2016; Kim et al., 2017; Liang et al., 2019).”
BackgroundMethodEnhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations
Salk, J. J., Schmitt, M. W., & Loeb, L. A. (2018) · Nature Reviews Genetics · doi:10.1038/nrg.2017.117 · Cited by 536 · see citing works
Directed evolution of CRISPR-Cas9 to increase its specificity
Lee, J. K., Jeong, E., Lee, J., Jung, M., Shin, E., Kim, Y.-H., Lee, K., Jung, I., Kim, D., Kim, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05477-x · Cited by 525 · see citing works
Self-citationDefining 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 508 · see citing works
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 · see citing works
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 · see citing works
Genome editing reveals a role for OCT4 in human embryogenesis
Fogarty, N. M. E., McCarthy, A., Snijders, K. E., Powell, B. E., Kubikova, N., Blakeley, P., Lea, R., Elder, K., Wamaitha, S. E., Kim, D., et al. (2017) · Nature · doi:10.1038/nature24033 · Cited by 392 · see citing works
Self-citationManghwar, H., Li, B., Ding, X. L., Hussain, A., Lindsey, K., Zhang, X., & Jin, S. (2020) · Advanced Science · doi:10.1002/advs.201902312 · Cited by 394 · see citing works
Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens
Morgens, D. W., Wainberg, M., Boyle, E. A., Ursu, O., Araya, C. L., Tsui, C. K., Haney, M. S., Hess, G. T., Han, K., Jeng, E. E., et al. (2017) · Nature Communications · doi:10.1038/ncomms15178 · Cited by 345 · see citing works
Increasing the specificity of CRISPR systems with engineered RNA secondary structures
Kocak, D. D., Josephs, E. A., Bhandarkar, V., Adkar, S. S., Kwon, J. B., & Gersbach, C. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0095-1 · Cited by 351 · see citing works
Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs
Listgarten, J., Weinstein, M., Kleinstiver, B. P., Sousa, A. A., Joung, J. K., Crawford, J., Gao, K., Hoang, L., Elibol, M., Doench, J. G., et al. (2018) · Nature Biomedical Engineering · doi:10.1038/s41551-017-0178-6 · Cited by 336 · see citing works
Zischewski, J., Fischer, R., & Bortesi, L. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2016.12.003 · Cited by 323 · see citing works
Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity
Tycko, J., Myer, V. E., & Hsu, P. D. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.07.004 · Cited by 304 · see citing works
Applying CRISPR/Cas for genome engineering in plants: the best is yet to come
Puchta, H. (2016) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2016.11.011 · Cited by 298 · see citing works
In Vivo Excision of HIV-1 Provirus by saCas9 and Multiplex Single-Guide RNAs in Animal Models
Yin, C., Zhang, T., Qu, X., Zhang, Y., Putatunda, R., Xiao, X., Li, F., Xiao, W., Zhao, H., Dai, S., et al. (2017) · Molecular Therapy · doi:10.1016/j.ymthe.2017.03.012 · Cited by 296 · see citing works
Genome-wide target specificities of CRISPR RNA-guided programmable deaminases
Kim, D., Lim, K., Kim, S., Yoon, S.-H., Kim, K., Ryu, S.-M., & Kim, J. (2017) · Nature Biotechnology · doi:10.1038/nbt.3852 · Cited by 275 · see citing works
Self-citationAbadi, S., Yan, W. X., Amar, D., & Mayrose, I. (2017) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005807 · Cited by 200 · see citing works
Genome-wide target specificity of CRISPR RNA-guided adenine base editors
Kim, D., Kim, D.-E., Lee, G., Cho, S.-I., & Kim, J. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0050-1 · Cited by 192 · see citing works
Self-citationIncorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity
Cromwell, C. R., Sung, K., Park, J., Krysler, A. R., Jovel, J., Kim, S. K., & Hubbard, B. P. (2018) · Nature Communications · doi:10.1038/s41467-018-03927-0 · Cited by 190 · see citing works
Self-citationHöijer, I., Emmanouilidou, A., Östlund, R., van Schendel, R., Bozorgpana, S., Tijsterman, M., Feuk, L., Gyllensten, U. B., den Hoed, M., & Ameur, A. (2022) · Nature Communications · doi:10.1038/s41467-022-28244-5 · Cited by 189 · see citing works
Dual-AAV delivering split prime editor system for in vivo genome editing
Zhi, S., Chen, Y., Wu, G., Wen, J., Wu, J., Liu, Q., Li, Y., Kang, R., Hu, S., Wang, J., et al. (2022) · Molecular Therapy · doi:10.1016/j.ymthe.2021.07.011 · Cited by 174 · see citing works
CRISPR-Cas9D10A nickase-based genotypic and phenotypic screening to enhance genome editing
Chiang, T.-W. W., le Sage, C., Larrieu, D., Demir, M., & Jackson, S. P. (2016) · Scientific Reports · doi:10.1038/srep24356 · Cited by 165 · see citing works
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Alkan, F., Wenzel, A., Anthon, C., Havgaard, J. H., & Gorodkin, J. (2018) · Genome biology · doi:10.1186/s13059-018-1534-x · Cited by 167 · see citing works
Evaluating and enhancing target specificity of gene-editing nucleases and deaminases
Kim, D., Luk, K., Wolfe, S. A., & Kim, J.-S. (2019) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-111730 · Cited by 171 · see citing works
Self-citationLau, C.-H., & Suh, Y. (2017) · F1000Research · doi:10.12688/f1000research.11243.1 · Cited by 161 · see citing works
Genome surgery using Cas9 ribonucleoproteins for the treatment of age-related macular degenerationPreprint
Kim, K., Park, S. W., Kim, J. H., Lee, S. H., Kim, D., Koo, T., Kim, K.-E., Kim, J. H., & Kim, J. (2017) · Genome Research · doi:10.1101/gr.219089.116 · Cited by 163 · see citing works
Self-citationUnbiased investigation of specificities of prime editing systems in human cells
Kim, D. Y., Moon, S. B., Ko, J., Kim, Y.-S., & Kim, D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa764 · Cited by 154 · see citing works
Self-citationGenome-wide profiling of adenine base editor specificity by EndoV-seq
Liang, P., Xie, X., Zhi, S., Sun, H., Zhang, X., Chen, Y., Chen, Y., Xiong, Y., Ma, W., Liu, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-018-07988-z · Cited by 148 · see citing works
Long Terminal Repeat CRISPR-CAR-Coupled “Universal” T Cells Mediate Potent Anti-leukemic Effects
Georgiadis, C., Preece, R., Nickolay, L. E., Etuk, A., Petrova, A., Ładoń, D., Danyi, A., Humphryes-Kirilov, N., Ajetunmobi, A., Kim, D., et al. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2018.02.025 · Cited by 136 · see citing works
Self-citationIn Silico Meets In Vivo : Towards Computational CRISPR-Based sgRNA Design
Chuai, G., Wang, Q., & Liu, Q. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2016.06.008 · Cited by 127 · see citing works
CRISPR/Cas9 Genome-Editing System in Human Stem Cells: Current Status and Future Prospects
Zhang, Z., Zhang, Y., Gao, F., Han, S., Cheah, K. S. E., Tse, H., & Lian, Q. (2017) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2017.09.009 · Cited by 116 · see citing works
Sherkatghanad, Z., Abdar, M., Charlier, J., & Makarenkov, V. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad131 · Cited by 117 · see citing works
CRISPR guide RNA design for research applications
Mohr, S. E., Hu, Y., Ewen‐Campen, B., Housden, B. E., Viswanatha, R., & Perrimon, N. (2016) · FEBS Journal · doi:10.1111/febs.13777 · Cited by 112 · see citing works
Bressan, R. B., Dewari, P. S., Kalantzaki, M., Gangoso, E., Matjusaitis, M., Garcia-Diaz, C., Blin, C., Grant, V., Bulstrode, H. J. C. J., Gogolok, S., et al. (2017) · Development · doi:10.1242/dev.140855 · Cited by 107 · see citing works
DIG-Seq: A genome-wide CRISPR off-target profiling method using chromatin DNA
Kim, D., & Kim, J.-S. (2018) · Genome Research · doi:10.1101/gr.236620.118 · Cited by 108 · see citing works
Self-citationTools for experimental and computational analyses of off-target editing by programmable nucleases
Bao, X. R., Pan, Y., Lee, C. M., Davis, T. H., & Bao, G. (2021) · Nature Protocols · doi:10.1038/s41596-020-00431-y · Cited by 106 · see citing works
An overview and metanalysis of machine and deep learning-based CRISPR gRNA design tools
Wang, J., Zhang, X., Cheng, L., & Luo, Y. (2019) · RNA Biology · doi:10.1080/15476286.2019.1669406 · Cited by 101 · see citing works
Jo, D. H., Song, D. W., Cho, C. S., Kim, U. G., Lee, K. J., Lee, K., Park, S. W., Kim, J., Kim, J. H., Kim, J., et al. (2019) · Science Advances · doi:10.1126/sciadv.aax1210 · Cited by 100 · see citing works
Self-citationPrime editing with genuine Cas9 nickases minimizes unwanted indels
Lee, J., Lim, K., Kim, A., Mok, Y. G., Chung, E., Cho, S.-I., Lee, J. M., & Kim, J. (2023) · Nature Communications · doi:10.1038/s41467-023-37507-8 · Cited by 96 · see citing works
Self-citationKoo, T., Park, S. W., Jo, D. H., Kim, D., Kim, J. H., Cho, H.-Y., Kim, J. H., Kim, J. H., & Kim, J. (2018) · Nature Communications · doi:10.1038/s41467-018-04175-y · Cited by 95 · see citing works
Self-citationEpigenome engineering: new technologies for precision medicine
Sgro, A., & Blancafort, P. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1000 · Cited by 96 · see citing works
CRISPR/Cas9 Landscape: Current State and Future Perspectives
Tyumentsev, A. I., Tyumentsev, A. I., & Акимкин, В. Г. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242216077 · Cited by 95 · see citing works
Efficient genome engineering approaches for the short-lived African turquoise killifish
Harel, I., Valenzano, D. R., & Brunet, A. (2016) · Nature Protocols · doi:10.1038/nprot.2016.103 · Cited by 86 · see citing works
Wang, Y., Liu, K. I., Sutrisnoh, N.-A. B., Srinivasan, H., Zhang, J., Li, J., Zhang, F., Richard, J. L. C., Xing, H., Shanmugam, R., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1445-x · Cited by 87 · see citing works
Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites
Tao, J., Wang, Q., Mendez‐Dorantes, C., Burns, K. H., & Chiarle, R. (2022) · Nature Communications · doi:10.1038/s41467-022-31322-3 · Cited by 88 · see citing works
Koo, T., Lu‐Nguyen, N., Malerba, A., Kim, E., Kim, D., Cappellari, O., Cho, H., Dickson, G., Popplewell, L. J., & Kim, J. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2018.03.018 · Cited by 80 · see citing works
Self-citationLopes, R., & Prasad, M. K. (2024) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2023.1339189 · Cited by 82 · see citing works
New traits in crops produced by genome editing techniques based on deletions
van de Wiel, C. C. M., Schaart, J. G., Lotz, L. A. P., & Smulders, M. J. M. (2017) · Plant Biotechnology Reports · doi:10.1007/s11816-017-0425-z · Cited by 80 · see citing works
Risk associated with off-target plant genome editing and methods for its limitation
Zhao, H., & Wolt, J. D. (2017) · Emerging Topics in Life Sciences · doi:10.1042/etls20170037 · Cited by 78 · see citing works
CRISPR–Cas9 a boon or bane: the bumpy road ahead to cancer therapeutics
Ghosh, D., Venkataramani, P., Nandi, S., & Bhattacharjee, S. (2019) · Cancer Cell International · doi:10.1186/s12935-019-0726-0 · Cited by 76 · see citing works
Cas9-nickase–mediated genome editing corrects hereditary tyrosinemia in rats
Shao, Y., Wang, L., Guo, N., Wang, S., Yang, L., Li, Y., Wang, M., Yin, S., Han, H., Zeng, L., et al. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000347 · Cited by 75 · see citing works
Atkins, A., Chung, C.-H., Allen, A., Dampier, W., Gurrola, T. E., Sariyer, I. K., Nonnemacher, M., & Wigdahl, B. (2021) · Frontiers in Genome Editing · doi:10.3389/fgeed.2021.673022 · Cited by 66 · see citing works
CRISPR-Cas9 genome engineering: Treating inherited retinal degeneration
Burnight, E. R., Giacalone, J. C., Cooke, J. A., Thompson, J. R., Bohrer, L. R., Chirco, K. R., Drack, A. V., Fingert, J. H., Worthington, K. S., Wiley, L. A., et al. (2018) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2018.03.003 · Cited by 75 · see citing works
Principles of and strategies for germline gene therapy
Wolf, D. P., Mitalipov, P. A., & Mitalipov, S. M. (2019) · Nature Medicine · doi:10.1038/s41591-019-0473-8 · Cited by 73 · see citing works
Gene therapies that restore dystrophin expression for the treatment of Duchenne muscular dystrophy
Robinson-Hamm, J. N., & Gersbach, C. A. (2016) · Human Genetics · doi:10.1007/s00439-016-1725-z · Cited by 69 · see citing works
Hasanzadeh, A., Hamblin, M. R., Kiani, J., Noori, H., Hardie, J. M., Karimi, M., & Shafiee, H. (2022) · Nano Today · doi:10.1016/j.nantod.2022.101665 · Cited by 69 · see citing works
Fine-Tuning Next-Generation Genome Editing Tools
Kanchiswamy, C. N., Maffei, M. E., Malnoy, M., Velasco, R., & Kim, J. (2016) · Trends in biotechnology · doi:10.1016/j.tibtech.2016.03.007 · Cited by 68 · see citing works
Self-citationControl of gene editing by manipulation of DNA repair mechanisms
Danner, E. W., Bashir, S., Yumlu, S., Wurst, W., Wefers, B., & Kühn, R. (2017) · Mammalian Genome · doi:10.1007/s00335-017-9688-5 · Cited by 69 · see citing works
Hwang, G., Lee, S., Oh, M., Kim, S., Habib, O., Jang, H., Kim, H. S., Kim, Y., Kim, C. H., Kim, S., et al. (2024) · Nature Biomedical Engineering · doi:10.1038/s41551-024-01277-5 · Cited by 72 · see citing works
Self-citationRecent Advances in Improving Gene-Editing Specificity through CRISPR–Cas9 Nuclease Engineering
Huang, X., Yang, D., Zhang, J., Xu, J., & Chen, Y. E. (2022) · Cells · doi:10.3390/cells11142186 · Cited by 65 · see citing works
Uemura, T., Mori, T., Kurihara, T., Kawase, S., Koike, R., Satoga, M., Cao, X., Li, X., Yanagawa, T., Sakurai, T., et al. (2016) · Scientific Reports · doi:10.1038/srep35861 · Cited by 65 · see citing works
Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
Höijer, I., Johansson, J., Gudmundsson, S., Chin, C.-S., Bunikis, I., Häggqvist, S., Emmanouilidou, A., Wilbe, M., den Hoed, M., Bondeson, M.-L., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02206-w · Cited by 64 · see citing works
Gene Editing and Genotoxicity: Targeting the Off-Targets
Blattner, G., Cavazza, A., Thrasher, A. J., & Turchiano, G. (2020) · Frontiers in Genome Editing · doi:10.3389/fgeed.2020.613252 · Cited by 62 · see citing works
Genome Editing with CRISPR-Cas9: Can It Get Any Better?
Haeussler, M., & Concordet, J. (2016) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2016.04.008 · Cited by 62 · see citing works
CRISPR system: Discovery, development and off-target detection
Chen, S., Yao, Y., Zhang, Y., & Fan, G. (2020) · Cellular Signalling · doi:10.1016/j.cellsig.2020.109577 · Cited by 61 · see citing works
Tracking-seq reveals the heterogeneity of off-target effects in CRISPR–Cas9-mediated genome editing
Zhu, M., Xu, R., Yuan, J., Wang, J., Ren, X., Cong, T., You, Y., Ju, A., Xu, L., Wang, H., et al. (2024) · Nature Biotechnology · doi:10.1038/s41587-024-02307-y · Cited by 60 · see citing works
Kujoth, G. C., Sullivan, T. D., Merkhofer, R. M., Lee, T.-J., Wang, H., Brandhorst, T. T., Wüthrich, M., & Klein, B. S. (2018) · mBio · doi:10.1128/mbio.00412-18 · Cited by 58 · see citing works
Zhang, G., Zeng, T., Dai, Z., & Dai, X. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.03.001 · Cited by 62 · see citing works
The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing
Bayat, H., Modarressi, M. H., & Rahimpour, A. (2017) · Current Microbiology · doi:10.1007/s00284-017-1406-8 · Cited by 56 · see citing works
Charlier, J., Nadon, R., & Makarenkov, V. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab112 · Cited by 56 · see citing works
CRISPR-DIPOFF: an interpretable deep learning approach for CRISPR Cas-9 off-target prediction
Toufikuzzaman, M., Samee, M. A. H., & Rahman, M. S. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbad530 · Cited by 58 · see citing works
Abbasi, A. F., Asim, M. N., & Dengel, A. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-024-06013-w · Cited by 57 · see citing works
Peng, H., Zheng, Y., Zhao, Z., Liu, T., & Li, J. (2018) · Bioinform. · doi:10.1093/bioinformatics/bty558 · Cited by 52 · see citing works
CRISPR therapeutic tools for complex genetic disorders and cancer (Review)
Baliou, S., Adamaki, M., Kyriakopoulos, A. M., Spandidos, D. A., Panayiotidis, M. I., Christodoulou, I., & Zoumpourlis, V. C. (2018) · International Journal of Oncology · doi:10.3892/ijo.2018.4434 · Cited by 48 · see citing works
Recent advances in genome editing of stem cells for drug discovery and therapeutic application
Lee, J., Bayarsaikhan, D., Bayarsaikhan, G., Kim, J., Schwarzbach, E., & Lee, B. (2020) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2020.107501 · Cited by 47 · see citing works
Self-citationAllosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage
Zuo, Z., & Liu, J. (2020) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2020.01.013 · Cited by 48 · see citing works
ABE8e adenine base editor precisely and efficiently corrects a recurrent COL7A1 nonsense mutation
Sheriff, A., Guri, I., Żebrowska-Różańska, P., Llopis-Hernández, V., Brooks, I. R., Tekkela, S., Subramaniam, K. S., Gebrezgabher, R., Naso, G., Petrova, A., et al. (2022) · Scientific Reports · doi:10.1038/s41598-022-24184-8 · Cited by 47 · see citing works
Technologies and Computational Analysis Strategies for CRISPR Applications
Clement, K., Hsu, J. Y., Canver, M. C., Joung, J. K., & Pinello, L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.06.012 · Cited by 44 · see citing works
Genome editing and the next generation of antiviral therapy
Stone, D., Niyonzima, N., & Jerome, K. R. (2016) · Human Genetics · doi:10.1007/s00439-016-1686-2 · Cited by 43 · see citing works
Making ends meet: targeted integration of DNA fragments by genome editing
Yamamoto, Y., & Gerbi, S. A. (2018) · Chromosoma · doi:10.1007/s00412-018-0677-6 · Cited by 43 · see citing works
Fortin, J., Tan, J., Gascoigne, K. E., Haverty, P. M., Forrest, W. F., Costa, M. R., & Martin, S. E. (2019) · Genome biology · doi:10.1186/s13059-019-1621-7 · Cited by 42 · see citing works
Digenome-seq web tool for profiling CRISPR specificity
Park, J., Childs, L. H., Kim, D., Hwang, G., Kim, S., Kim, S., Kim, J., & Bae, S. (2017) · Nature Methods · doi:10.1038/nmeth.4262 · Cited by 42 · see citing works
Self-citationPetri, K., Kim, D. Y., Sasaki, K. E., Canver, M. C., Wang, X., Shah, H., Lee, H., Horng, J. E., Clement, K., Iyer, S., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.05.438458 · Cited by 42 · see citing works
Self-citationGene editing of the multi-copy H2A.B gene and its importance for fertility
Anuar, N. D., Kurscheid, S., Field, M. A., Zhang, L., Rebar, E. J., Gregory, P. D., Buchou, T., Bowles, J., Koopman, P. A., Tremethick, D. J., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1633-3 · Cited by 41 · see citing works
CRISPRoffT: comprehensive database of CRISPR/Cas off-targets
Wang, G., Liu, X., Wang, A., Wen, J., Kim, P., Song, Q., Liu, X., & Zhou, X. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1025 · Cited by 41 · see citing works
Kim, D., Kang, B., & Kim, J. (2021) · Nature Protocols · doi:10.1038/s41596-020-00453-6 · Cited by 41 · see citing works
Self-citationEslami-Mossallam, B., Klein, M., van der Smagt, C. P., van der Sanden, K., Jones, S. K., Hawkins, J. A., Finkelstein, I. J., & Depken, M. (2022) · Nature Communications · doi:10.1038/s41467-022-28994-2 · Cited by 40 · see citing works
Tycko, J., Barrera, L. A., Huston, N. C., Friedland, A. E., Wu, X., Gootenberg, J. S., Abudayyeh, O. O., Myer, V. E., Wilson, C. J., & Hsu, P. D. (2018) · Nature Communications · doi:10.1038/s41467-018-05391-2 · Cited by 38 · see citing works
Diving into marine genomics with CRISPR/Cas9 systems
Momose, T., & Concordet, J. (2016) · Marine Genomics · doi:10.1016/j.margen.2016.10.003 · Cited by 39 · see citing works
crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays
Störtz, F., & Minary, P. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa885 · Cited by 37 · see citing works
Effective and precise adenine base editing in mouse zygotes
Liang, P., Sun, H., Zhang, X., Xie, X., Zhang, J., Bai, Y., Ouyang, X., Zhi, S., Xiong, Y., Ma, W., et al. (2018) · Protein & Cell · doi:10.1007/s13238-018-0566-z · Cited by 36 · see citing works
Zhang, C., Li, N., Rao, L., Li, J., Liu, Q., & Tian, C. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02321-21 · Cited by 36 · see citing works
AcrIIA5 Suppresses Base Editors and Reduces Their Off-Target Effects
Liang, M., Sui, T., Liu, Z., Chen, M., Liu, H., Shan, H., Lai, L., & Li, Z. (2020) · Cells · doi:10.3390/cells9081786 · Cited by 33 · see citing works
- Authors
- Kim, D., Kim, S., Kim, S., Park, J., & Kim, J.-S.
- Affiliations
- Seoul National University (KR)
- Hanyang University (KR)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2016-01-19
- Volume
- 26
- Issue
- 3
- Pages
- 406-415
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC4772022
- OpenAlex
- W2273244674
- Cited by
- 208
- References
- 37
- Citations by year
- 2026: 8 · 2025: 15 · 2024: 13 · 2023: 12 · 2022: 17 · 2021: 23 · 2020: 29 · 2019: 22 · 2018: 26 · 2017: 21 · 2016: 22
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Seoul National University Open Repository (Seoul National University) (submittedVersion)
- Funders
- IBS (IBS-R021-D1)
- 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
- CRISPR/Cas9, off-target effects, single guide RNA, indel frequency, target site selection, genome editing
- MeSH terms
- Binding Sites, Humans, Protein Binding, Reproducibility of Results, Genome, Human, Gene Targeting, Genomics, INDEL Mutation, Position-Specific Scoring Matrices, High-Throughput Nucleotide Sequencing, Nucleotide Motifs, Mutation Rate, 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
