The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
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.
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“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
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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
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
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
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
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
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
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
Bae, S., Park, J., & Kim, J.-S. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu048 · Cited by 2,339
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Items 201–209 of 209
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) · Figshare · doi:10.6084/m9.figshare.13316830
Kwon, J., Kim, M., Hwang, W., Jo, A., Hwang, G.-H., Jung, M., Kim, U. G., Cui, G., Kim, H. S., Eom, J.-H., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22601906
Self-citationKwon, J., Kim, M., Hwang, W. C., Jo, A., Hwang, G.-H., Jung, M., Kim, U. G., Cui, G., Kim, H. S., Eom, J.-H., et al. (2023) · Figshare · doi:10.6084/m9.figshare.22601897
Self-citationHöijer, 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) · Figshare · doi:10.6084/m9.figshare.13316827
Shi, Y., Yin, J., Ning, S., Yuan, J., Yang, D., & Chuai, G. (2026) · BMC Genomics · doi:10.1186/s12864-026-13003-3
19Chapter 2 Revolutionizing Genomics with Artificial Intelligence
Verma, K., Duhan, P., Bansal, P., Sharma, A., & Sharma, A. K. (2026) · De Gruyter eBooks · doi:10.1515/9783112214275-002
CRISPR/Cas based genome editing for liver diseases: Promise and challenge
Guan, J., Yang, M., Yang, X., He, Q., Wang, B., & Zhan, C. (2026) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2026.09.027
Shruthy, N. S., Dong, C.-D., Chen, Y.-T., Hsieh, S.-L., Singhania, R. R., & Patel, A. K. (2026) · Bioresources and Bioprocessing · doi:10.1186/s40643-026-01136-y
Nonclinical Evaluation of Gene-Editing Products
(2026) · Elsevier eBooks · doi:10.1016/b978-0-443-48612-8.00016-6
Metadata
- 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
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