Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
Open accessAbstract
Summary: Clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies have revolutionized human genome engineering and opened countless possibilities to basic science, synthetic biology and gene therapy. Albeit the enormous potential of these tools, their performance is far from perfect. It is essential to perform a posterior careful analysis of the gene editing experiment. However, there are no computational tools for genome editing assessment yet, and current experimental tools lack sensitivity and flexibility. We present a platform to assess the quality of a genome editing experiment only with three mouse clicks. The method evaluates next-generation data to quantify and characterize insertions, deletions and homologous recombination. CRISPR Genome Analyzer provides a report for the locus selected, which includes a quantification of the edited site and the analysis of the different alterations detected. The platform maps the reads, estimates and locates insertions and deletions, computes the allele replacement efficiency and provides a report integrating all the information. Availability and implementation: CRISPR-GA Web is available at http://crispr-ga.net . Documentation on CRISPR-GA instructions can be found at http://crispr-ga.net/documentation.html Contact: mguell@genetics.med.harvard.edu
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The deep-sequencing detection limit reflects the Illumina platform's inherent error rate, up to 0.4%.
“The limit of detection in these experiments is based on the inherent error rate of the Illumina platform (up to 0.4%), which has previously been described for genome editing experiment analyzed by NGS71–73.”
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 [73]
The Introduction says CRISPR-GA uses Illumina MiSeq sequencing, and the Implementation section describes filtering reads with sequencing errors. The Conclusions give a detection limit for CRISPR-GA, but no passage identifies an inherent Illumina error rate of up to 0.4% or says that rate determines the detection limit in the citing paper’s experiments (searched: 0.4%, Illumina error rate, detection limit). (LLM, conf=0.75)
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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 · 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
Self-citation<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · 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
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
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 · see citing works
Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems
DiCarlo, J. E., Norville, J. E., Mali, P., Rios, X., Aach, J., & Church, G. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt135 · Cited by 1,566 · see citing works
Self-citationEfficient genome editing in plants using a CRISPR/Cas system
Feng, Z., Zhang, B., Ding, W., Liu, X., Yang, D., Wei, P., Cao, F., Zhu, S., Zhang, F., Mao, Y., et al. (2013) · Cell Research · doi:10.1038/cr.2013.114 · Cited by 1,070 · see citing works
Niu, Y., Shen, B., Cui, Y., Chen, Y., Wang, J., Wang, L., Kang, Y., Zhao, X., Si, W., Li, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.027 · Cited by 1,033 · see citing works
Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
Esvelt, K. M., Mali, P., Braff, J. L., Moosburner, M., Yaung, S. J., & Church, G. M. (2013) · Nature Methods · doi:10.1038/nmeth.2681 · Cited by 786 · see citing works
Self-citationHeritable gene targeting in the mouse and rat using a CRISPR-Cas system
Li, D., Qiu, Z., Shao, Y., Chen, Y., Guan, Y., Liu, M., Li, Y., Wang, L., Wang, L., Lu, X., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2661 · Cited by 639 · see citing works
Comparison of DNA Sequences with Protein Sequences
Pearson, W. R., Wood, T. C., Zhang, Z., & Miller, W. (1997) · Genomics · doi:10.1006/geno.1997.4995 · Cited by 601 · see citing works
Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly
Kim, H. J., Lee, H. J., Kim, H., Cho, S. W., & Kim, J.-S. (2009) · Genome Research · doi:10.1101/gr.089417.108 · Cited by 466 · see citing works
Optimization of scarless human stem cell genome editing
Yang, L., Güell, M., Byrne, S., Yang, J. L., Angeles, A. D. L., Mali, P., Aach, J., Kim-Kiselak, C., Briggs, A. W., Rios, X., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt555 · Cited by 374 · see citing works
Self-citationHighly Efficient Genome Modifications Mediated by CRISPR/Cas9 in Drosophila
Yu, Z., Ren, M., Wang, Z., Zhang, B., Rong, Y. S., Jiao, R., & Gao, G. (2013) · Genetics · doi:10.1534/genetics.113.153825 · Cited by 339 · see citing works
Mutation detection using Surveyor™ nuclease
Qiu, P., Shandilya, H., D'Alessio, J. M., O’Connor, K. C., Durocher, J. A., & Gerard, G. F. (2004) · BioTechniques · doi:10.2144/04364pf01 · Cited by 299 · see citing works
Huang, M. C., Cheong, W. C., Lim, L. S., & Li, M. (2012) · Electrophoresis · doi:10.1002/elps.201100460 · Cited by 40 · see citing works
Flagged first, then by citations
1 of the 19 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
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 · see citing works
Easy quantitative assessment of genome editing by sequence trace decomposition
Brinkman, E. K., Chen, T., Amendola, M., & van Steensel, B. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku936 · Cited by 2,390 · see citing works
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 1,632 · see citing works
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 · see citing works
Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9
Niu, D., Wei, H., Lin, L., George, H., Wang, T., Lee, I., Zhao, H., Wang, Y., Kan, Y., Shrock, E. L., et al. (2017) · Science · doi:10.1126/science.aan4187 · Cited by 765 · see citing works
Self-citationGenome-wide inactivation of porcine endogenous retroviruses (PERVs)
Yang, L., Güell, M., Niu, D., George, H., Lesha, E., Grishin, D., Aach, J., Shrock, E. L., Xu, W., Poci, J., et al. (2015) · Science · doi:10.1126/science.aad1191 · Cited by 604 · see citing works
Self-citationHi-TOM: a platform for high-throughput tracking of mutations induced by CRISPR/Cas systems
Liu, Q., Wang, C., Jiao, X., Zhang, H., Song, L., Li, Y., Gao, C., & Wang, K. (2018) · Science China Life Sciences · doi:10.1007/s11427-018-9402-9 · Cited by 503 · see citing works
Analyzing CRISPR genome-editing experiments with CRISPResso
Pinello, L., Canver, M. C., Hoban, M. D., Orkin, S. H., Kohn, D. B., Bauer, D. E., & Yuan, G. (2016) · Nature Biotechnology · doi:10.1038/nbt.3583 · Cited by 450 · see citing works
Cas-analyzer: an online tool for assessing genome editing results using NGS data
Park, J., Lim, K., Kim, J., & Bae, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw561 · Cited by 400 · 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
CRISPR/cas9 genome editing in wheat
Kim, D., Alptekin, B., & Budak, H. (2018) · Functional & Integrative Genomics · doi:10.1007/s10142-017-0572-x · Cited by 365 · see citing works
Lee, B., Lee, K., Panda, S., Gonzales-Rojas, R., Chong, A., Bugay, V., Park, H. M., Brenner, R., Murthy, N., & Lee, H. Y. (2018) · Nature Biomedical Engineering · doi:10.1038/s41551-018-0252-8 · Cited by 361 · see citing works
Staahl, B. T., Benekareddy, M., Coulon-Bainier, C., Banfal, A. A., Floor, S. N., Sabo, J. K., Urnes, C., Munares, G. A., Ghosh, A., & Doudna, J. A. (2017) · Nature Biotechnology · doi:10.1038/nbt.3806 · Cited by 355 · see citing works
Rapid reverse genetic screening using CRISPR in zebrafish
Shah, A. N., Davey, C. F., Whitebirch, A. C., Miller, A. C., & Moens, C. B. (2015) · Nature Methods · doi:10.1038/nmeth.3360 · Cited by 343 · 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
Easy quantification of template-directed CRISPR/Cas9 editing
Brinkman, E. K., Kousholt, A. N., Harmsen, T., Leemans, C., Chen, T., Jonkers, J., & van Steensel, B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky164 · Cited by 197 · see citing works
CRIS.py: A Versatile and High-throughput Analysis Program for CRISPR-based Genome Editing
Connelly, J. P., & Pruett‐Miller, S. M. (2019) · Scientific Reports · doi:10.1038/s41598-019-40896-w · Cited by 174 · see citing works
Rasul, M. F., Hussen, B. M., Salihi, A. B., Ismael, B. S., Jalal, P. J., Zanichelli, A., Jamali, E., Baniahmad, A., Ghafouri‐Fard, S., Basiri, A., et al. (2022) · Molecular Cancer · doi:10.1186/s12943-021-01487-4 · Cited by 180 · see citing works
Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells
Byrne, S. M., Ortiz, L., Mali, P., Aach, J., & Church, G. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1246 · Cited by 164 · see citing works
Self-citationIn Situ Gene Therapy via AAV-CRISPR-Cas9-Mediated Targeted Gene Regulation
Moreno, A. M., Fu, X., Zhu, J., Katrekar, D., Shih, Y.-R. V., Marlett, J., Cabotaje, J., Tat, J., Naughton, J., Lisowski, L., et al. (2018) · Molecular Therapy · doi:10.1016/j.ymthe.2018.04.017 · Cited by 159 · see citing works
CrispRVariants charts the mutation spectrum of genome engineering experiments
Lindsay, H. A., Burger, A., Biyong, B., Felker, A., Hess, C., Zaugg, J., Chiavacci, E., Anders, C., Jínek, M., Mosimann, C., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3628 · Cited by 155 · see citing works
Characteristics of Genome Editing Mutations in Cereal Crops
Zhu, C., Bortesi, L., Baysal, C., Twyman, R. M., Fischer, R., Capell, T., Schillberg, S., & Christou, P. (2016) · Trends in Plant Science · doi:10.1016/j.tplants.2016.08.009 · Cited by 149 · see citing works
Synthetically modified guide RNA and donor DNA are a versatile platform for CRISPR-Cas9 engineering
Lee, K., Mackley, V. A., Rao, A., Chong, A. T., DeWitt, M. A., Corn, J. E., & Murthy, N. (2017) · eLife · doi:10.7554/elife.25312 · Cited by 141 · see citing works
CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity
Carrington, B., Varshney, G. K., Burgess, S. M., & Sood, R. B. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv802 · Cited by 139 · see citing works
Genome editing: A perspective on the application of CRISPR/Cas9 to study human diseases (Review)
Rodríguez-Rodríguez, D. R., Ram�rez‐Sol�s, R., Garza‐Elizondo, M. A., Garza‐Rodr�guez, M., & Barrera-Saldaña, H. A. (2019) · International Journal of Molecular Medicine · doi:10.3892/ijmm.2019.4112 · Cited by 133 · see citing works
Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files
Rausch, T., Fritz, M. H.-Y., Untergasser, A., & Benes, V. (2020) · BMC Genomics · doi:10.1186/s12864-020-6635-8 · Cited by 130 · see citing works
Computational Tools and Resources for CRISPR/Cas Genome Editing
Li, C., Chu, W., Gill, R. A., Sang, S., Shi, Y., Hu, X., Yang, Y., Zaman, Q. U., & Zhang, B. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.02.006 · Cited by 131 · see citing works
In 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
Expanding the CRISPR Toolbox in Zebrafish for Studying Development and Disease
Liu, K., Petree, C., Requena, T., Varshney, P., & Varshney, G. K. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00013 · Cited by 124 · see citing works
Lee, C. M., Cradick, T. J., Fine, E. J., & Bao, G. (2016) · Molecular Therapy · doi:10.1038/mt.2016.1 · Cited by 122 · see citing works
Lonowski, L. A., Narimatsu, Y., Riaz, A., Delay, C. M., Yang, Z., Niola, F., Duda, K., Ober, E. A., Clausen, H., Wandall, H. H., et al. (2017) · Nature Protocols · doi:10.1038/nprot.2016.165 · Cited by 109 · see citing works
Tools 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
Wiley, L. A., Burnight, E. R., Songstad, A. E., Drack, A. V., Mullins, R. F., Stone, E. M., & Tucker, B. A. (2014) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2014.10.002 · Cited by 107 · see citing works
Understanding and Editing the Zebrafish Genome
Varshney, G. K., Sood, R. B., & Burgess, S. M. (2015) · Advances in genetics · doi:10.1016/bs.adgen.2015.09.002 · Cited by 100 · see citing works
Genome Editing in Human Stem Cells
Byrne, S. M., Mali, P., & Church, G. M. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-801185-0.00006-4 · Cited by 96 · see citing works
Self-citationTargeting miRNA by CRISPR/Cas in cancer: advantages and challenges
Hussen, B. M., Rasul, M. F., Abdullah, S. R., Hidayat, H. J., Faraj, G. S. H., Ali, F. A., Salihi, A. B., Baniahmad, A., Ghafouri‐Fard, S., Rahman, M., et al. (2023) · Military Medical Research · doi:10.1186/s40779-023-00468-6 · Cited by 97 · see citing works
BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment
Boel, A., Steyaert, W., Rocker, N. D., Menten, B., Callewaert, B. L., Paepe, A. D., Coucke, P. J., & Willaert, A. (2016) · Scientific Reports · doi:10.1038/srep30330 · Cited by 88 · see citing works
Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments
Canver, M. C., Haeussler, M., Bauer, D. E., Orkin, S. H., Sanjana, N. E., Shalem, O., Yuan, G., Zhang, F., Concordet, J., & Pinello, L. (2018) · Nature Protocols · doi:10.1038/nprot.2018.005 · Cited by 87 · see citing works
Genotyping genome‐edited mutations in plants using CRISPR ribonucleoprotein complexes
Liang, Z., Chen, K., Yan, Y., Zhang, Y., & Gao, C. (2018) · Plant Biotechnology Journal · doi:10.1111/pbi.12938 · Cited by 78 · see citing works
You, Q., Zhong, Z., Ren, Q., Hassan, F., Zhang, Y., & Zhang, T. (2018) · International Journal of Biological Sciences · doi:10.7150/ijbs.24581 · Cited by 72 · see citing works
Current Bioinformatics Tools to Optimize CRISPR/Cas9 Experiments to Reduce Off-Target Effects
Naeem, M., & Alkhnbashi, O. S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24076261 · Cited by 70 · see citing works
Yin, C., Zhang, T., Li, F., Yang, F., Putatunda, R., Young, W., Khalili, K., Hu, W., & Zhang, Y. (2016) · AIDS · doi:10.1097/qad.0000000000001079 · Cited by 67 · see citing works
Digital PCR to assess gene-editing frequencies (GEF-dPCR) mediated by designer nucleases
Mock, U., Hauber, I., & Fehse, B. (2016) · Nature Protocols · doi:10.1038/nprot.2016.027 · Cited by 66 · see citing works
Gene editing by CRISPR/Cas9 in the obligatory outcrossing Medicago sativa
Gao, R., Feyissa, B. A., Croft, M., & Hannoufa, A. (2018) · Planta · doi:10.1007/s00425-018-2866-1 · Cited by 67 · see citing works
Shabbir, R., Javed, T., Afzal, I., Sabagh, A. E., Ali, A., Vicente, Ó., & Chen, P. (2021) · Agronomy · doi:10.3390/agronomy11061042 · Cited by 65 · see citing works
CRISPR/Cas9-gene editing approaches in plant breeding
Saini, H., Thakur, R., Gill, R., Tyagi, K., & Goswami, M. (2023) · GM crops & food · doi:10.1080/21645698.2023.2256930 · Cited by 64 · see citing works
Application of CRISPR/Cas9 genome editing to the study and treatment of disease
Pellagatti, A., Dolatshad, H., Valletta, S., & Boultwood, J. (2015) · Archives of Toxicology · doi:10.1007/s00204-015-1504-y · Cited by 65 · see citing works
Oligonucleotide conjugated multi-functional adeno-associated viruses
Katrekar, D., Moreno, A. M., Chen, G., Worlikar, A., & Mali, P. (2018) · Scientific Reports · doi:10.1038/s41598-018-21742-x · Cited by 57 · see citing works
TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap
McShan, A. C., Devlin, C. A., Morozov, G. I., Overall, S. A., Moschidi, D., Akella, N., Procko, E., & Sgourakis, N. G. (2021) · Nature Communications · doi:10.1038/s41467-021-23225-6 · Cited by 56 · see citing works
Computational Tools and Resources Supporting CRISPR-Cas Experiments
Śledziński, P., Nowaczyk, M., & Olejniczak, M. (2020) · Cells · doi:10.3390/cells9051288 · Cited by 54 · see citing works
AGEseq: Analysis of Genome Editing by Sequencing
Xue, L., & Tsai, C. (2015) · Molecular Plant · doi:10.1016/j.molp.2015.06.001 · Cited by 54 · see citing works
Heritability of targeted gene modifications induced by plant-optimized CRISPR systems
Mao, Y., Botella, J. R., & Zhu, J. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2380-1 · Cited by 55 · see citing works
Find and cut-and-transfer (FiCAT) mammalian genome engineering
Pallarès-Masmitjà, M., Ivančić, D., Mir-Pedrol, J., Jaraba-Wallace, J., Tagliani, T., Oliva, B., Rahmeh, A. A., Sánchez-Mejías, A., & Güell, M. (2021) · Nature Communications · doi:10.1038/s41467-021-27183-x · Cited by 54 · see citing works
Self-citationCRISPR-Mediated Editing of the B Cell Receptor in Primary Human B Cells
Greiner, V., Bou-Puerto, R., Liu, S., Herbel, C., Carmona, E. M., & Goldberg, M. S. (2019) · iScience · doi:10.1016/j.isci.2019.01.032 · Cited by 50 · see citing works
Indiková, I., & Indik, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa561 · Cited by 47 · see citing works
CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline
Wang, X., Tilford, C. A., Neuhaus, I., Mintier, G. A., Guo, Q. J., Feder, J. N., & Kirov, S. A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx518 · Cited by 45 · 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
Ramadan, M., Alariqi, M., Ma, Y., Li, Y., Liu, Z., Zhang, R., Jin, S., Min, L., & Zhang, X. (2021) · Plant Methods · doi:10.1186/s13007-021-00712-x · Cited by 45 · see citing works
Amit, I., Iancu, O., Levy-Jurgenson, A., Kurgan, G., McNeill, M., Rettig, G. R., Allen, D. G., Breier, D., Haim, N. B., Wang, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22417-4 · Cited by 42 · see citing works
A Comparison of Techniques to Evaluate the Effectiveness of Genome Editing
Germini, D., Tsfasman, T., Zakharova, V., Sjakste, N., Lipinski, M., & Vassetzky, Y. S. (2017) · Trends in biotechnology · doi:10.1016/j.tibtech.2017.10.008 · Cited by 41 · see citing works
Sharma, S. K., Gupta, O. P., Pathaw, N., Sharma, D., Maibam, A., Sharma, P., Sanasam, J., Karkute, S. G., Kumar, S., & Bhattacharjee, B. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.751512 · Cited by 43 · see citing works
Applications of CRISPR-Cas9 mediated genome engineering
Yang, X. P. (2015) · Military Medical Research · doi:10.1186/s40779-015-0038-1 · Cited by 37 · see citing works
Impact of Genetic Variation on CRISPR-Cas Targeting
Canver, M. C., Joung, J. K., & Pinello, L. (2018) · The CRISPR Journal · doi:10.1089/crispr.2017.0016 · Cited by 36 · see citing works
Li, B., Ren, N., Yang, L., Liu, J., & Huang, Q. (2019) · Scientific Reports · doi:10.1038/s41598-019-55463-6 · Cited by 34 · see citing works
Self-citationDynamics of Indel Profiles Induced by Various CRISPR/Cas9 Delivery Methods
Kosicki, M., Rajan, S. S., Lorenzetti, F. C., Wandall, H. H., Narimatsu, Y., Metzakopian, E., & Bennett, E. (2017) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2017.09.003 · Cited by 34 · see citing works
Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools
Laganà, A., Shasha, D. E., & Croce, C. M. (2014) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2014.00065 · Cited by 33 · see citing works
Ferdous, M. A., Islam, S. I., Habib, N., Almehmadi, M. M., Allahyani, M. A., Alsaiari, A. A., & Shafie, A. (2022) · Microorganisms · doi:10.3390/microorganisms10102012 · Cited by 38 · see citing works
High-throughput methods for genome editing: the more the better
Huang, Y., Shang, M., Liu, T., & Wang, K. (2022) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiac017 · Cited by 30 · see citing works
CRISPR‐Mediated Gene Targeting of Human Induced Pluripotent Stem Cells
Byrne, S. M., & Church, G. M. (2015) · Current Protocols in Stem Cell Biology · doi:10.1002/9780470151808.sc05a08s35 · Cited by 30 · see citing works
Self-citationCRISPR/Cas-Mediated Genome Editing for Sugarcane Improvement
Mall, A. K., Manimekalai, R., Misra, V., Pandey, H., Srivastava, S., & Sharma, A. (2024) · Sugar Tech · doi:10.1007/s12355-023-01352-2 · Cited by 29 · see citing works
A Web Portal for Rice Crop Improvements
Baurley, J. W., Budiarto, A., Kacamarga, M. F., & Pardamean, B. (2018) · International Journal of Web Portals · doi:10.4018/ijwp.2018070102 · Cited by 28 · see citing works
Dabrowska, M., Czubak, K., Juzwa, W., Krzyżosiak, W. J., Olejniczak, M., & Kozłowski, P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky505 · Cited by 25 · see citing works
CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver
Kaltenbacher, T., Löprich, J., Maresch, R., Weber, J., Müller, S., Oellinger, R., Groß, N., Griger, J., Krätzig, N. D. A., Avramopoulos, P., et al. (2022) · Nature Protocols · doi:10.1038/s41596-021-00677-0 · Cited by 24 · see citing works
Periwal, V. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw052 · Cited by 25 · see citing works
CRISPR genome editing using computational approaches: A survey
Alipanahi, R., Safari, L., & Khanteymoori, A. (2023) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.1001131 · Cited by 23 · see citing works
Pallarès-Masmitjà, M., Knödlseder, N., & Güell, M. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9170-9_1 · Cited by 22 · see citing works
Self-citationCRISPRpic: fast and precise analysis for CRISPR-induced mutations via p refixed i ndex c ounting
Lee, H., Chang, H. Y., Cho, S. W., & Ji, H. P. (2020) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaa012 · Cited by 22 · see citing works
Wang, Y., Li, R., Zhu, Z., Yuan, Z., Wang, C., Wang, L., Zhang, D., & Yang, L. (2022) · Sensors and Actuators B Chemical · doi:10.1016/j.snb.2022.132781 · Cited by 20 · see citing works
Self-citationIida, M., Suzuki, M., Sakane, Y., Nishide, H., Uchiyama, I., Yamamoto, T., Suzuki, K., & Fujii, S. (2020) · Genes to Cells · doi:10.1111/gtc.12775 · Cited by 20 · see citing works
Özçelik, F., Dündar, M. S., Yildirim, A. B., HENEHAN, G. T. M., Vicente, O., Sánchez-Alcázar, J. A., Gökçe, N., Yildirim, D. T., Bingol, N. N., Plaseska‐Karanfilska, D., et al. (2024) · Functional & Integrative Genomics · doi:10.1007/s10142-024-01417-9 · Cited by 21 · see citing works
In Vivo Editing of the Adult Mouse Liver Using CRISPR/Cas9 and Hydrodynamic Tail Vein Injection
Niola, F., Dagnæs‐Hansen, F., & Frödin, M. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9170-9_20 · Cited by 17 · see citing works
The era of editing plant genomes using CRISPR/Cas: A critical appraisal
Bhat, M. A., Bhat, M. A., Kumar, V., Wani, I. A., Bashir, H., Shah, A. A., Rahman, S., & Jan, A. T. (2020) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2020.09.013 · Cited by 17 · see citing works
In silico Method in CRISPR/Cas System: An Expedite and Powerful Booster
Zhang, Y., Zhao, G., Ahmed, F. Y. H., Yi, T., Hu, S., Cai, T., & Liao, Q. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.584404 · Cited by 17 · see citing works
SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing
Li, F., Tan, X., Li, S., Chen, S., Liu, L., Huang, J., Li, G., Lu, Z., Wu, J., Zeng, D., et al. (2025) · Molecular Plant · doi:10.1016/j.molp.2025.03.002 · Cited by 16 · see citing works
Systematic Comparison of Computational Tools for Sanger Sequencing-Based Genome Editing Analysis
Aoki, K., Yamasaki, M., Umezono, R., Hamamoto, T., & Kamachi, Y. (2024) · Cells · doi:10.3390/cells13030261 · Cited by 15 · see citing works
Veeranagouda, Y., Debono, D., Fournet, H., Thill, G., & Didier, M. (2018) · Current Protocols in Molecular Biology · doi:10.1002/cpmb.53 · Cited by 15 · see citing works
Genome editing and bioinformatics
Nakamae, K., & Bono, H. U. (2022) · Gene and Genome Editing · doi:10.1016/j.ggedit.2022.100018 · Cited by 14 · see citing works
Evaluation of genome and base editing tools in maize protoplasts
Fierlej, Y., Jacquier, N. M. A., Guille, L., Just, J., Montes, É., Richard, C., Loue-Manifel, J., Depège‐Fargeix, N., Gaillard, A., Widiez, T., et al. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.1010030 · Cited by 14 · see citing works
CRISPR-SE: a brute force search engine for CRISPR design
Li, B., Chen, P. B., & Diao, Y. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab013 · Cited by 13 · see citing works
Integrated design, execution, and analysis of arrayed and pooled CRISPR genome editing experimentsPreprint
Canver, M. C., Haeussler, M., Bauer, D. E., Orkin, S. H., Sanjana, N. E., Shalem, O., Yuan, G., Zhang, F., Concordet, J., & Pinello, L. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/125245 · Cited by 13 · see citing works
Huang, L., Wang, D., Chen, H., Hu, J., Dai, X., Liu, C., Li, A., Shen, X., Chen, Q., Sun, H., et al. (2023) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2023.03.010 · Cited by 12 · see citing works
Biswas, S., Li, R., Hong, J., Zhao, X., Yuan, Z., Zhang, D., & Shi, J. (2020) · Theoretical and Applied Genetics · doi:10.1007/s00122-020-03600-5 · Cited by 12 · see citing works
Targeted Genome Editing Using DNA-Free RNA-Guided Cas9 Ribonucleoprotein for CHO Cell Engineering
Shin, J., Lee, N., Cho, S., & Cho, B. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-7795-6_8 · Cited by 12 · see citing works
Schröpfer, S., & Flachowsky, H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222212611 · Cited by 11 · see citing works
CRISPR-Cas guide RNA indel analysis using CRISPResso2 with Nanopore sequencing data
McFarlane, G. R., Cortez, J. V., & Bogema, D. R. (2024) · BMC Research Notes · doi:10.1186/s13104-024-06861-1 · Cited by 10 · see citing works
Guzmán‐López, M. H., Marín‐Sanz, M., Sánchez‐León, S., & Barro, F. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222313076 · Cited by 10 · see citing works
CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing
Sanvicente-García, M., García-Valiente, A., Jouide, S., Jaraba-Wallace, J., Bautista, È., Escobosa, M., Sánchez-Mejías, A., & Güell, M. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011137 · Cited by 10 · see citing works
Self-citationCRISPR/Cas9: The Leading Edge of Genome Editing Technology
Sakuma, T., & Yamamoto, T. (2014) · Springer eBooks · doi:10.1007/978-4-431-55227-7_2 · Cited by 10 · see citing works
Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0
Assa, G., Kalter, N., Rosenberg, M., Beck, A., Markovich, O., Gontmakher, T., Hendel, A., & Yakhini, Z. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae651 · Cited by 9 · see citing works
- Authors
- Güell, M., Yang, L., & Church, G. M.
- Affiliations
- Harvard University (US)
- Corresponding author
- Church, George M.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-07-01
- Volume
- 30
- Issue
- 20
- Pages
- 2968-2970
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4184265
- OpenAlex
- W2161871693
- Semantic Scholar
- 513d19c6d364f6a5d5c30c3a2edd41581cc2f9b0
- Cited by
- 142
- References
- 19
- Citations by year
- 2026: 1 · 2025: 8 · 2024: 9 · 2023: 11 · 2022: 11 · 2021: 16 · 2020: 18 · 2019: 13 · 2018: 16 · 2017: 11 · 2016: 13 · 2015: 8 · 2014: 7
- FWCI
- 5.33
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (P50HG005550, HG005550)
- 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 › Genomics and Phylogenetic Studies
- Keywords
- CRISPR gene editing, indels, homologous recombination, next-generation sequencing data analysis, web-based analysis tool
- MeSH terms
- Alleles, Genetic Engineering, Humans, User-Computer Interface, Genome, Human, Genomics, High-Throughput Nucleotide Sequencing, Clustered Regularly Interspaced Short Palindromic Repeats
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