The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
CRISPR/Cas Systems in Genome Editing: Methodologies and Tools for sgRNA Design, Off‐Target Evaluation, and Strategies to Mitigate Off‐Target Effects
Abstract
Life sciences have been revolutionized by genome editing (GE) tools, including zinc finger nucleases, transcription activator‐Like effector nucleases, and CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas (CRISPR‐associated) systems, which make the targeted modification of genomic DNA of all organisms possible. CRISPR/Cas systems are being widely used because of their accuracy, efficiency, and cost‐effectiveness. Various classes of CRISPR/Cas systems have been developed, but their extensive use may be hindered by off‐target effects. Efforts are being made to reduce the off‐target effects of CRISPR/Cas9 by generating various CRISPR/Cas systems with high fidelity and accuracy. Several approaches have been applied to detect and evaluate the off‐target effects. Here, the current GE tools, the off‐target effects generated by GE technology, types of off‐target effects, mechanisms of off‐target effects, major concerns, and outcomes of off‐target effects in plants and animals are summarized. The methods to detect off‐target effects, tools for single‐guide RNA (sgRNA) design, evaluation and prediction of off‐target effects, and strategies to increase the on‐target efficiency and mitigate the off‐target impact on intended genome‐editing outcomes are summarized.
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 check wasn’t confident either way, so it gives no verdict — never disputed.
In the citing paper
“Generally speaking, studies revealed that GC content of between 40% and 60%, truncated (short length of sgRNA), and incorporation of 2ʹ-O-methyl-3ʹ-phosphonoacetate in the sgRNA ribose-phosphate backbone are the preferred methods to increase genome editing efficiency of CRISPR/Cas-9.67,68”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [67]
Experimental — accuracy not yet measuredIn the citing paper
“Generally speaking, studies revealed that GC content of between 40% and 60%, truncated (short length of sgRNA), and incorporation of 2ʹ-O-methyl-3ʹ-phosphonoacetate in the sgRNA ribose-phosphate backbone are the preferred methods to increase genome editing efficiency of CRISPR/Cas-9.67,68”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [67]
In the citing paper
“Generally speaking, studies revealed that GC content of between 40% and 60%, truncated (short length of sgRNA), and incorporation of 2ʹ-O-methyl-3ʹ-phosphonoacetate in the sgRNA ribose-phosphate backbone are the preferred methods to increase genome editing efficiency of CRISPR/Cas-9.67,68”
From Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing (2021) · cites this paper as [67]
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
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
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
The new frontier of genome engineering with CRISPR-Cas9
Doudna, J. A., & Charpentier, E. (2014) · Science · doi:10.1126/science.1258096 · Cited by 7,062
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
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.022 · Cited by 5,016
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
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
Flagged first, then by citations
Research works printed but not linked: 98
- 10.1016/j.tig.2018.05.004 · DOI
- 10.1038/nbt.3659 · DOI · Paper page
- 10.1186/s13059-018-1534-x · DOI
- 10.1038/nbt.2507 · DOI · Paper page
- 10.1038/nbt.2650 · DOI · Paper page
- 10.1104/pp.15.00636 · DOI · Paper page
- 10.1016/j.molcel.2017.09.029 · DOI · Paper page
- 10.1016/j.jgg.2017.04.009 · DOI
- 10.1186/s13578-019-0298-7 · DOI
- 10.1038/nbt.4102 · DOI
- 10.1093/nar/gkt714 · DOI · Paper page
- 10.1016/B978-0-12-801185-0.00002-7 · DOI
- 10.1038/s41576-018-0059-1 · DOI · Paper page
- 10.1038/s41587-019-0050-1 · DOI
- 10.1038/ncomms15790 · DOI · Paper page
- 10.1038/s41467-018-04580-3 · DOI · Paper page
- 10.3389/fpls.2018.01245 · DOI
- 10.1186/s13059-018-1458-5 · DOI
- 10.1038/nature13011 · DOI · Paper page
- 10.1073/pnas.1402597111 · DOI
- 10.1038/ncomms13350 · DOI
- 10.1038/ncomms12778 · DOI
- 10.1242/dev.099085 · DOI
- 10.1038/s41594-019-0188-z · DOI
- 10.1186/s13059-016-1012-2 · DOI · Paper page
- 10.1038/s41592-018-0011-5 · DOI
- 10.1038/s41421-019-0088-8 · DOI
- 10.1038/nmeth.2845 · DOI
- 10.1093/bioinformatics/bty558 · DOI
- 10.1111/nph.13470 · DOI
- 10.1186/s13578-017-0148-4 · DOI
- 10.1016/j.biotechadv.2014.12.006 · DOI
- 10.1038/523158a · DOI
- 10.1038/nmeth.4293 · DOI
- 10.1042/ETLS20170037 · DOI
- 10.1038/s41477-019-0406-z · DOI
- 10.1093/nsr/nwz005 · DOI
- 10.1016/j.gene.2019.03.019 · DOI
- 10.3390/ijms161024751 · DOI
- 10.1073/pnas.1700557114 · DOI
- 10.1038/s41422-019-0159-2 · DOI
- 10.1073/pnas.1400822111 · DOI
- 10.1111/pbi.12200 · DOI
- 10.1038/s41598-017-00578-x · DOI
- 10.1111/pbi.13020 · DOI
- 10.1038/ncomms12463 · DOI
- 10.1038/nmeth.3284 · DOI · Paper page
- 10.1038/nmeth.2408 · DOI · Paper page
- 10.1038/nm.4313 · DOI
- 10.1038/s41467-018-07988-z · DOI · Paper page
- 10.1093/nar/gkq791 · DOI
- 10.1038/s41586-018-0500-9 · DOI
- 10.1111/febs.13248 · DOI
- 10.1093/bioinformatics/btu048 · DOI · Paper page
- 10.1038/s41467-017-01732-9 · DOI
- 10.1038/s41594-018-0051-7 · DOI
- 10.1111/pbi.13025 · DOI
- 10.1093/nar/gkv575 · DOI · Paper page
- 10.1093/nar/gku410 · DOI
- 10.1038/srep25516 · DOI
- 10.1093/nar/gky354 · DOI
- 10.1016/j.molp.2017.06.004 · DOI
- 10.1016/j.cell.2015.09.038 · DOI · Paper page
- 10.1016/j.molp.2017.01.003 · DOI
- 10.1038/nmeth.2812 · DOI
- 10.1093/nar/gkw407 · DOI
- Aach J., 2014, BioRxiv, 005074
- 10.1186/s13059-018-1445-x · DOI
- 10.1186/s12920-018-0394-2 · DOI
- 10.1038/nrg.2016.28 · DOI
- 10.1101/gr.219089.116 · DOI
- 10.1016/j.cell.2013.08.021 · DOI · Paper page
- 10.1038/nchembio.1793 · DOI
- 10.1038/nbt.3155 · DOI
- 10.1002/anie.201606123 · DOI
- 10.1016/j.cell.2016.12.009 · DOI
- 10.1038/s41467-018-05477-x · DOI · Paper page
- Li D., 2019, Cell Biol. Toxicol., 1
- 10.1073/pnas.1714640114 · DOI
- 10.1126/sciadv.aax5717 · DOI
- 10.1038/s41587-019-0236-6 · DOI
- 10.1038/s41586-019-1314-0 · DOI · Paper page
- 10.1016/j.molp.2019.03.011 · DOI
- 10.1038/emm.2016.111 · DOI
- 10.1038/srep26685 · DOI
- 10.1042/BCJ20170793 · DOI
- 10.1126/science.aaq0180 · DOI · Paper page
- 10.1016/j.jmb.2018.06.029 · DOI
- 10.1038/nbt.3596 · DOI
- 10.1038/nbt.3609 · DOI · Paper page
- 10.1371/journal.pbio.2005595 · DOI
- 10.1073/pnas.1810062115 · DOI
- 10.1101/gr.162339.113 · DOI · Paper page
- 10.1038/nbt.2916 · DOI · Paper page
- 10.4161/15384101.2014.949201 · DOI
- 10.1038/srep12327 · DOI
- 10.1093/nar/gkw398 · DOI
- 10.1021/acscentsci.9b00020 · DOI
Cited by
Sorted by citations
Mechanism and Applications of CRISPR/Cas-9-Mediated Genome Editing
Mengstie, M. A., & Wondimu, B. Z. (2021) · Biologics: Targets and Therapy · doi:10.2147/btt.s326422 · Cited by 478
Chehelgerdi, M., Chehelgerdi, M., Khorramian-Ghahfarokhi, M., Shafieizadeh, M., Mahmoudi, E., Eskandari, F., Rashidi, M., Arshi, A., & Mokhtari-Farsani, A. (2024) · Molecular Cancer · doi:10.1186/s12943-023-01925-5 · Cited by 251
Lin, J., Zhang, Z., Zhang, S., Chen, J., & Wong, K. (2020) · Advanced Science · doi:10.1002/advs.201903562 · Cited by 101
Metadata
- Authors
- Manghwar, H., Li, B., Ding, X., Hussain, A., Lindsey, K., Zhang, X., & Jin, S.
- Affiliations
- National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan Hubei 430070 P. R. China
- Department of Biosciences Durham University Durham DH1 3LE UK
- ORCID
- Jin, Shuangxia
- Venue
- Advanced Science
- Publisher
- Wiley
- Published
- 2020-02-06
- Volume
- 7
- Issue
- 6
- ISSN
- 2198-3844
- PMC
- PMC7080517
- Cited by
- 347
- References
- 41
- Language
- en
- Funders
- National R&D Project of Transgenic Crops of Ministry of Science and Technology of China (2018ZX08010-05B, 2016ZX08005-001-006, 2019ZX08010-003)
- National Key Research and Development Plan (2016YFD0100203-9)
- Consulting Project of China Academy of Engineering (2018-XY-63)
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