메뉴 건너뛰기




Volumn 17, Issue 1, 2016, Pages

Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR

Author keywords

[No Author keywords available]

Indexed keywords

GUIDE RNA; SMALL NUCLEAR RNA; U6 SMALL NUCLEAR RNA;

EID: 84977522458     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-016-1012-2     Document Type: Article
Times cited : (1188)

References (54)
  • 1
    • 84900388716 scopus 로고    scopus 로고
    • RNA events. Cas9 targeting and the CRISPR revolution
    • Barrangou R. RNA events. Cas9 targeting and the CRISPR revolution. Science. 2014;344:707-8.
    • (2014) Science , vol.344 , pp. 707-708
    • Barrangou, R.1
  • 2
    • 84923221641 scopus 로고    scopus 로고
    • Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors
    • Wang X, Wang Y, Wu X, Wang J, Wang Y, Qiu Z, et al. Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors. Nat Biotechnol. 2015;33:175-8.
    • (2015) Nat Biotechnol , vol.33 , pp. 175-178
    • Wang, X.1    Wang, Y.2    Wu, X.3    Wang, J.4    Wang, Y.5    Qiu, Z.6
  • 3
    • 84923266604 scopus 로고    scopus 로고
    • GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
    • Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol. 2015;33:187-97.
    • (2015) Nat Biotechnol , vol.33 , pp. 187-197
    • Tsai, S.Q.1    Zheng, Z.2    Nguyen, N.T.3    Liebers, M.4    Topkar, V.V.5    Thapar, V.6
  • 4
    • 84900458436 scopus 로고    scopus 로고
    • Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila
    • Gratz SJ, Ukken FP, Rubinstein CD, Thiede G, Donohue LK, Cummings AM, et al. Highly specific and efficient CRISPR/Cas9-catalyzed homology-directed repair in Drosophila. Genetics. 2014;196:961-71.
    • (2014) Genetics , vol.196 , pp. 961-971
    • Gratz, S.J.1    Ukken, F.P.2    Rubinstein, C.D.3    Thiede, G.4    Donohue, L.K.5    Cummings, A.M.6
  • 6
    • 84919762182 scopus 로고    scopus 로고
    • Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila
    • Ren X, Yang Z, Xu J, Sun J, Mao D, Hu Y, et al. Enhanced specificity and efficiency of the CRISPR/Cas9 system with optimized sgRNA parameters in Drosophila. Cell Rep. 2014;9:1151-62.
    • (2014) Cell Rep , vol.9 , pp. 1151-1162
    • Ren, X.1    Yang, Z.2    Xu, J.3    Sun, J.4    Mao, D.5    Hu, Y.6
  • 8
  • 10
    • 84893287073 scopus 로고    scopus 로고
    • E-CRISP: fast CRISPR target site identification
    • Heigwer F, Kerr G, Boutros M. E-CRISP: fast CRISPR target site identification. Nat Methods. 2014;11:122-3.
    • (2014) Nat Methods , vol.11 , pp. 122-123
    • Heigwer, F.1    Kerr, G.2    Boutros, M.3
  • 11
    • 84896308706 scopus 로고    scopus 로고
    • Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
    • Bae S, Park J, Kim J-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30:1473-5.
    • (2014) Bioinformatics , vol.30 , pp. 1473-1475
    • Bae, S.1    Park, J.2    Kim, J.-S.3
  • 12
    • 84907573408 scopus 로고    scopus 로고
    • CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems
    • Zhu LJ, Holmes BR, Aronin N, Brodsky MH. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems. PLoS One. 2014;9:e108424.
    • (2014) PLoS One , vol.9 , pp. e108424
    • Zhu, L.J.1    Holmes, B.R.2    Aronin, N.3    Brodsky, M.H.4
  • 15
    • 84922596582 scopus 로고    scopus 로고
    • CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants
    • Lei Y, Lu L, Liu H-Y, Li S, Xing F, Chen L-L. CRISPR-P: a web tool for synthetic single-guide RNA design of CRISPR-system in plants. Mol Plant. 2014;7:1494-6.
    • (2014) Mol Plant , vol.7 , pp. 1494-1496
    • Lei, Y.1    Lu, L.2    Liu, H.-Y.3    Li, S.4    Xing, F.5    Chen, L.-L.6
  • 16
    • 84907486023 scopus 로고    scopus 로고
    • GT-Scan: identifying unique genomic targets
    • O'Brien A, Bailey TL. GT-Scan: identifying unique genomic targets. Bioinformatics. 2014;30:2673-5.
    • (2014) Bioinformatics , vol.30 , pp. 2673-2675
    • O'Brien, A.1    Bailey, T.L.2
  • 17
    • 84898889321 scopus 로고    scopus 로고
    • CasOT: a genome-wide Cas9/gRNA off-target searching tool
    • Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, et al. CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics. 2014;30:1180-2.
    • (2014) Bioinformatics , vol.30 , pp. 1180-1182
    • Xiao, A.1    Cheng, Z.2    Kong, L.3    Zhu, Z.4    Lin, S.5    Gao, G.6
  • 18
    • 84929142256 scopus 로고    scopus 로고
    • CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
    • Naito Y, Hino K, Bono H, Ui-Tei K. CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics. 2015;31:1120-3.
    • (2015) Bioinformatics , vol.31 , pp. 1120-1123
    • Naito, Y.1    Hino, K.2    Bono, H.3    Ui-Tei, K.4
  • 19
    • 84903549014 scopus 로고    scopus 로고
    • sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites
    • Xie S, Shen B, Zhang C, Huang X, Zhang Y. sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential off-target cleavage sites. PLoS One. 2014;9:e100448.
    • (2014) PLoS One , vol.9 , pp. e100448
    • Xie, S.1    Shen, B.2    Zhang, C.3    Huang, X.4    Zhang, Y.5
  • 20
    • 84924333960 scopus 로고    scopus 로고
    • "Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs
    • Pliatsika V, Rigoutsos I. "Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs. Biol Direct. 2015;10:4.
    • (2015) Biol Direct , vol.10 , pp. 4
    • Pliatsika, V.1    Rigoutsos, I.2
  • 21
    • 84929377243 scopus 로고    scopus 로고
    • CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences
    • Prykhozhij SV, Rajan V, Gaston D, Berman JN. CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One. 2015;10:e0119372.
    • (2015) PLoS One , vol.10 , pp. e0119372
    • Prykhozhij, S.V.1    Rajan, V.2    Gaston, D.3    Berman, J.N.4
  • 22
    • 84938902048 scopus 로고    scopus 로고
    • Flexible guide-RNA design for CRISPR applications using Protospacer Workbench
    • MacPherson CR, Scherf A. Flexible guide-RNA design for CRISPR applications using Protospacer Workbench. Nat Biotechnol. 2015;33:805-6.
    • (2015) Nat Biotechnol , vol.33 , pp. 805-806
    • MacPherson, C.R.1    Scherf, A.2
  • 23
    • 84938829555 scopus 로고    scopus 로고
    • Sequence determinants of improved CRISPR sgRNA design
    • Xu H, Xiao T, Chen C-H, Li W, Meyer CA, Wu Q, et al. Sequence determinants of improved CRISPR sgRNA design. Genome Res. 2015;25(8):1147-57.
    • (2015) Genome Res , vol.25 , Issue.8 , pp. 1147-1157
    • Xu, H.1    Xiao, T.2    Chen, C.-H.3    Li, W.4    Meyer, C.A.5    Wu, Q.6
  • 24
    • 84940501210 scopus 로고    scopus 로고
    • Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach
    • Chari R, Mali P, Moosburner M, Church GM. Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach. Nat Methods. 2015;12:823-6.
    • (2015) Nat Methods , vol.12 , pp. 823-826
    • Chari, R.1    Mali, P.2    Moosburner, M.3    Church, G.M.4
  • 25
    • 84926433352 scopus 로고    scopus 로고
    • Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design
    • Farboud B, Meyer BJ. Dramatic enhancement of genome editing by CRISPR/Cas9 through improved guide RNA design. Genetics. 2015;199:959-71.
    • (2015) Genetics , vol.199 , pp. 959-971
    • Farboud, B.1    Meyer, B.J.2
  • 27
    • 84960392032 scopus 로고    scopus 로고
    • Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq
    • Kim D, Kim S, Kim S, Park J, Kim J-S. Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq. Genome Res. 2016;26:406-15.
    • (2016) Genome Res , vol.26 , pp. 406-415
    • Kim, D.1    Kim, S.2    Kim, S.3    Park, J.4    Kim, J.-S.5
  • 28
    • 84923275611 scopus 로고    scopus 로고
    • Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases
    • Frock RL, Hu J, Meyers RM, Ho Y-J, Kii E, Alt FW. Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases. Nat Biotechnol. 2015;33:179-86.
    • (2015) Nat Biotechnol , vol.33 , pp. 179-186
    • Frock, R.L.1    Hu, J.2    Meyers, R.M.3    Ho, Y.-J.4    Kii, E.5    Alt, F.W.6
  • 29
    • 84891710947 scopus 로고    scopus 로고
    • Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
    • Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 2014;24:132-41.
    • (2014) Genome Res , vol.24 , pp. 132-141
    • Cho, S.W.1    Kim, S.2    Kim, Y.3    Kweon, J.4    Kim, H.S.5    Bae, S.6
  • 31
    • 84902141229 scopus 로고    scopus 로고
    • Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs
    • Gagnon JA, Valen E, Thyme SB, Huang P, Ahkmetova L, Pauli A, et al. Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One. 2014;9:e98186.
    • (2014) PLoS One , vol.9 , pp. e98186
    • Gagnon, J.A.1    Valen, E.2    Thyme, S.B.3    Huang, P.4    Ahkmetova, L.5    Pauli, A.6
  • 33
    • 84923846574 scopus 로고    scopus 로고
    • 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 HR, et al. Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells. Nat Methods. 2015;12:237-43.
    • (2015) Nat Methods , vol.12 , pp. 237-243
    • Kim, D.1    Bae, S.2    Park, J.3    Kim, E.4    Kim, S.5    Yu, H.R.6
  • 34
    • 84957605863 scopus 로고    scopus 로고
    • Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
    • Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF, et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol. 2016;34:184-91.
    • (2016) Nat Biotechnol , vol.34 , pp. 184-191
    • Doench, J.G.1    Fusi, N.2    Sullender, M.3    Hegde, M.4    Vaimberg, E.W.5    Donovan, K.F.6
  • 35
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 36
    • 84929494345 scopus 로고    scopus 로고
    • CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool
    • Stemmer M, Thumberger T, Del Sol KM, Wittbrodt J, Mateo JL. CCTop: an intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PLoS One. 2015;10:e0124633.
    • (2015) PLoS One , vol.10 , pp. e0124633
    • Stemmer, M.1    Thumberger, T.2    Sol, K.M.3    Wittbrodt, J.4    Mateo, J.L.5
  • 37
    • 84983752643 scopus 로고    scopus 로고
    • Cas9-chromatin binding information enables more accurate CRISPR off-target prediction
    • Singh R, Kuscu C, Quinlan A, Qi Y, Adli M. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction. Nucleic Acids Res. 2015;43:e118.
    • (2015) Nucleic Acids Res , vol.43 , pp. e118
    • Singh, R.1    Kuscu, C.2    Quinlan, A.3    Qi, Y.4    Adli, M.5
  • 38
    • 84892749369 scopus 로고    scopus 로고
    • Genetic screens in human cells using the CRISPR-Cas9 system
    • Wang T, Wei JJ, Sabatini DM, Lander ES. Genetic screens in human cells using the CRISPR-Cas9 system. Science. 2014;343:80-4.
    • (2014) Science , vol.343 , pp. 80-84
    • Wang, T.1    Wei, J.J.2    Sabatini, D.M.3    Lander, E.S.4
  • 40
    • 84930611267 scopus 로고    scopus 로고
    • High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
    • Varshney GK, Pei W, LaFave MC, Idol J, Xu L, Gallardo V, et al. High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res. 2015;25:1030-42.
    • (2015) Genome Res , vol.25 , pp. 1030-1042
    • Varshney, G.K.1    Pei, W.2    LaFave, M.C.3    Idol, J.4    Xu, L.5    Gallardo, V.6
  • 41
    • 84949233942 scopus 로고    scopus 로고
    • High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities
    • Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G, et al. High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell. 2015;163:1515-26.
    • (2015) Cell , vol.163 , pp. 1515-1526
    • Hart, T.1    Chandrashekhar, M.2    Aregger, M.3    Steinhart, Z.4    Brown, K.R.5    MacLeod, G.6
  • 42
    • 84977485598 scopus 로고    scopus 로고
    • Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona.
    • Gandhi S, Christiaen L, Stolfi A. Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona. bioRxiv. 2016. doi: http://dx.doi.org/10.1101/041632.
    • (2016) bioRxiv.
    • Gandhi, S.1    Christiaen, L.2    Stolfi, A.3
  • 43
    • 84955598451 scopus 로고    scopus 로고
    • Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system
    • Liu X, Homma A, Sayadi J, Yang S, Ohashi J, Takumi T. Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system. Sci Rep. 2016;6:19675.
    • (2016) Sci Rep , vol.6 , pp. 19675
    • Liu, X.1    Homma, A.2    Sayadi, J.3    Yang, S.4    Ohashi, J.5    Takumi, T.6
  • 44
    • 84941030856 scopus 로고    scopus 로고
    • Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi
    • Housden BE, Valvezan AJ, Kelley C, Sopko R, Hu Y, Roesel C, et al. Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi. Sci Signal. 2015;8:rs9.
    • (2015) Sci Signal , vol.8 , pp. rs9
    • Housden, B.E.1    Valvezan, A.J.2    Kelley, C.3    Sopko, R.4    Hu, Y.5    Roesel, C.6
  • 45
    • 84945926658 scopus 로고    scopus 로고
    • WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system
    • Wong N, Liu W, Wang X. WU-CRISPR: characteristics of functional guide RNAs for the CRISPR/Cas9 system. Genome Biol. 2015;16:218.
    • (2015) Genome Biol , vol.16 , pp. 218
    • Wong, N.1    Liu, W.2    Wang, X.3
  • 46
    • 84874628805 scopus 로고    scopus 로고
    • Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides
    • Wefers B, Meyer M, Ortiz O, Hrabé de Angelis M, Hansen J, Wurst W, et al. Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides. Proc Natl Acad Sci U S A. 2013;110:3782-7.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 3782-3787
    • Wefers, B.1    Meyer, M.2    Ortiz, O.3    Hrabé de Angelis, M.4    Hansen, J.5    Wurst, W.6
  • 47
    • 84947471999 scopus 로고    scopus 로고
    • Identification and characterization of essential genes in the human genome
    • Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, et al. Identification and characterization of essential genes in the human genome. Science. 2015;350:1096-101.
    • (2015) Science , vol.350 , pp. 1096-1101
    • Wang, T.1    Birsoy, K.2    Hughes, N.W.3    Krupczak, K.M.4    Post, Y.5    Wei, J.J.6
  • 49
    • 84873729095 scopus 로고    scopus 로고
    • Multiplex genome engineering using CRISPR/Cas systems
    • Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339:819-23.
    • (2013) Science , vol.339 , pp. 819-823
    • Cong, L.1    Ran, F.A.2    Cox, D.3    Lin, S.4    Barretto, R.5    Habib, N.6
  • 50
    • 84907942795 scopus 로고    scopus 로고
    • Characterization of dystrophin deficient rats: a new model for Duchenne muscular dystrophy
    • Larcher T, Lafoux A, Tesson L, Remy S, Thepenier V, François V, et al. Characterization of dystrophin deficient rats: a new model for Duchenne muscular dystrophy. PLoS One. 2014;9:e110371.
    • (2014) PLoS One , vol.9 , pp. e110371
    • Larcher, T.1    Lafoux, A.2    Tesson, L.3    Remy, S.4    Thepenier, V.5    François, V.6
  • 51
    • 84957890081 scopus 로고    scopus 로고
    • Correction of the auditory phenotype in C57BL/6 N mice via CRISPR/Cas9-mediated homology directed repair
    • Mianné J, Chessum L, Kumar S, Aguilar C, Codner G, Hutchison M, et al. Correction of the auditory phenotype in C57BL/6 N mice via CRISPR/Cas9-mediated homology directed repair. Genome Med. 2016;8:16.
    • (2016) Genome Med , vol.8 , pp. 16
    • Mianné, J.1    Chessum, L.2    Kumar, S.3    Aguilar, C.4    Codner, G.5    Hutchison, M.6
  • 54
    • 84898665052 scopus 로고    scopus 로고
    • Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library
    • Koike-Yusa H, Li Y, Tan E-P, Velasco-Herrera MDC, Yusa K. Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library. Nat Biotechnol. 2014;32:267-73.
    • (2014) Nat Biotechnol , vol.32 , pp. 267-273
    • Koike-Yusa, H.1    Li, Y.2    Tan, E.-P.3    Velasco-Herrera, M.D.C.4    Yusa, K.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.