The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing
Open accessAbstract
Genome editing has attracted wide interest for the generation of cellular models of disease using human pluripotent stem cells and other cell types. CRISPR-Cas systems and TALENs can target desired genomic sites with high efficiency in human cells, but recent publications have led to concern about the extent to which these tools may cause off-target mutagenic effects that could potentially confound disease-modeling studies. Using CRISPR-Cas9 and TALEN targeted human pluripotent stem cell clones, we performed whole-genome sequencing at high coverage in order to assess the degree of mutagenesis across the entire genome. In both types of clones, we found that off-target mutations attributable to the nucleases were very rare. From this analysis, we suggest that, although some cell types may be at risk for off-target mutations, the incidence of such effects in human pluripotent stem cells may be sufficiently low and thus not a significant concern for disease modeling and other applications.
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 says what the claim attributes to it.
In the citing paper
“To further complicate this issue, reprogramming and genetic engineering itself have also been implicated in increasing genomic variation.169–171”
From Developments in stem cell-derived islet replacement therapy for treating type 1 diabetes (2023) · cites this paper as [170]
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
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895
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
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEMPreprint
Li, H. (2014) · arXiv (Cornell University) · doi:10.6084/m9.figshare.963153.v1 · Cited by 5,155
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
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
The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Stransky, N., Egloff, A. M., Tward, A. D., Kostic, A. D., Cibulskis, K., Sivachenko, A., Kryukov, G. V., Lawrence, M. S., Sougnez, C. L., McKenna, A., et al. (2011) · Science · doi:10.1126/science.1208130 · Cited by 2,541
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Beneš, V., & Korbel, J. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts378 · Cited by 2,438
A TALE nuclease architecture for efficient genome editing
Miller, J. C., Tan, S., Qiao, G., Barlow, K. A., Wang, J., Xia, D. F., Meng, X., Paschon, D. E., Leung, E., Hinkley, S. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1755 · Cited by 2,098
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
Targeted 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
Mali, 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 2×
“…been demonstrated to produce off-target effects, i.e., mutagenesis at sites in the genome other than the desired on-target site (Hockemeyer et al., 2011; Mussolino et al., 2011; Fu et al., 2013; Hsu et al., 2013; Mali et al., 2013a; Pattanayak et al., 2013; Cradick et al., 2013; Cho et al., 2014).”
Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011) · Genome Research · doi:10.1101/gr.114876.110 · Cited by 1,658
LUMPY: a probabilistic framework for structural variant discovery
Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r84 · Cited by 1,544
Pattanayak, 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 4×
“…been demonstrated to produce off-target effects, i.e., mutagenesis at sites in the genome other than the desired on-target site (Hockemeyer et al., 2011; Mussolino et al., 2011; Fu et al., 2013; Hsu et al., 2013; Mali et al., 2013a; Pattanayak et al., 2013; Cradick et al., 2013; Cho et al., 2014).”
InfluentialAnalysis 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
Somatic coding mutations in human induced pluripotent stem cells
Gore, A., Li, Z., Fung, H.-L., Young, J. E., Agarwal, S., Antosiewicz-Bourget, J., Canto, I., Giorgetti, A., Israel, M. A., Kiskinis, E., et al. (2011) · Nature · doi:10.1038/nature09805 · Cited by 1,273
Genetic engineering of human pluripotent cells using TALE nucleases
Hockemeyer, D. F., Wang, H., Kiani, S., Lai, C. S., Gao, Q., Cassady, J. P., Cost, G. J., Zhang, L., Santiago, Y., Miller, J. C., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1927 · Cited by 1,161
Copy number variation and selection during reprogramming to pluripotency
Hussein, S. M. I., Batada, N. N., Vuoristo, S., Ching, R. W., Autio, R., Närvä, E., Ng, S. H. S., Sourour, M., Hämäläinen, R. H., Olsson, C., et al. (2011) · Nature · doi:10.1038/nature09871 · Cited by 980
A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity
Mussolino, C., Morbitzer, R., Lütge, F., Dannemann, N., Lahaye, T., & Cathomen, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr597 · Cited by 714
Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells
Yusa, K., Rashid, S. T., Strick‐Marchand, H., Varela, I., Liu, P.-Q., Paschon, D. E., Miranda, E., Ordóñez, A., Hannan, N. R. F., Rouhani, F. J., et al. (2011) · Nature · doi:10.1038/nature10424 · Cited by 647
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
Talkowski, M. E., Rosenfeld, J. A., Blumenthal, I., Pillalamarri, V., Chiang, C., Heilbut, A., Ernst, C., Hanscom, C., Rossin, E., Lindgren, A. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.028 · Cited by 577
Self-citationA TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models
Ding, Q., Lee, Y., Schaefer, E. A. K., Peters, D., Veres, A., Kim, K. J., Kuperwasser, N., Motola, D., Meissner, T. B., Hendriks, W. T. J., et al. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.11.011 · Cited by 515
Self-citationDing, Q., Regan, S. N., Xia, Y., Oostrom, L. A., Cowan, C. A., & Musunuru, K. (2013) · Cell Stem Cell · doi:10.1016/j.stem.2013.03.006 · Cited by 459
Self-citationChiang, C., Jacobsen, J. C., Ernst, C., Hanscom, C., Heilbut, A. M., Blumenthal, I., Mills, R. E., Kirby, A. W., Lindgren, A. M., Rudiger, S. R., et al. (2012) · Nature Genetics · doi:10.1038/ng.2202 · Cited by 261
Self-citationTalkowski, M. E., Ernst, C., Heilbut, A. M., Chiang, C., Hanscom, C., Lindgren, A. M., Kirby, A. W., Liu, S., Muddukrishna, B., Ohsumi, T. K., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.03.013 · Cited by 177
Self-citationGenetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy
Howden, S. E., Gore, A., Li, Z., Fung, H.-L., Nisler, B. S., Nie, J., Chen, G., McIntosh, B. E., Gulbranson, D. R., Diol, N. R., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1103388108 · Cited by 153
Genome editing of human pluripotent stem cells to generate human cellular disease models
Musunuru, K. (2013) · Disease Models & Mechanisms · doi:10.1242/dmm.012054 · Cited by 148
Self-citationInversion variants in the human genome: role in disease and genome architecture
Feuk, L. (2010) · Genome Medicine · doi:10.1186/gm132 · Cited by 100
Genome editing in human pluripotent stem cells
Peters, D. (2014) · StemBook · doi:10.3824/stembook.1.94.1 · Cited by 37
Cited by
Sorted by citations
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
GUIDE-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
Induced pluripotent stem cell technology: a decade of progress.
Shi, Y., Inoue, H., Wu, J. C., & Yamanaka, S. (2017) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.245 · Cited by 1,525
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
Metadata
- Authors
- Veres, A., Gosis, B. S., Ding, Q., Collins, R., Ragavendran, A., Brand, H., Erdin, S., Cowan, C. A., Talkowski, M. E., & Musunuru, K.
- Affiliations
- Harvard University (US)
- Massachusetts General Hospital (US)
- Broad Institute (US)
- Corresponding author
- Musunuru, Kiran
- ORCID
- Venue
- Cell Stem Cell
- Publisher
- Elsevier BV
- Published
- 2014-07
- Volume
- 15
- Issue
- 1
- Pages
- 27-30
- ISSN
- 1875-9777 (ISSN-L)
- 1934-5909
- PMC
- PMC4082799
- OpenAlex
- W1974343902
- Cited by
- 474
- References
- 32
- Citations by year
- 2026: 6 · 2025: 8 · 2024: 10 · 2023: 24 · 2022: 24 · 2021: 32 · 2020: 33 · 2019: 43 · 2018: 46 · 2017: 61 · 2016: 72 · 2015: 86 · 2014: 29
- FWCI
- 33.92
- Type
- journal article
- Language
- en
- Update notices
- erratum (2014-08-07)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell stem cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- National Heart, Lung, and Blood Institute (U01HL100408, R00HL098364, R01HL118744)
- National Institute of Mental Health (R00MH095867)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK097768)
- 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 › Pluripotent Stem Cells Research
- Keywords
- off-target mutations, CRISPR/Cas9, TALEN, genome editing, human pluripotent stem cells, mutagenesis, disease modeling, whole genome sequencing
- MeSH terms
- Sortilin, Base Sequence, Clone Cells, Endonucleases, Genetic Engineering, Humans, Molecular Sequence Data, Mutation, Organ Specificity, Incidence, Genome, Sequence Analysis, DNA, Adaptor Proteins, Vesicular Transport, Pluripotent Stem Cells, 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
