A digital pcr-based method for efficient and highly specific screening of genome edited cells

PLoS ONE

Volumn 11, Issue 4, 2016, Pages

  Findlay, Scott D ^a,b   Vincent, Krista M ^a,b   Berman, Jennifer R ^c   Postovit, Lynne Marie ^b  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

^c BIO RAD LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; PROTEIN NODAL; SECRETED FRIZZLED RELATED PROTEIN 1; TRANSCRIPTION ACTIVATOR LIKE EFFECTOR NUCLEASE;

ACCURACY; ARTICLE; CONTROLLED STUDY; CRISPR CAS SYSTEM; DROPLET DIGITAL POLYMERASE CHAIN REACTION; GENE MUTATION; GENETIC ENGINEERING; GENETIC SCREENING; GENOME EDITING; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; HUMAN CELL; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; PROCESS DEVELOPMENT; PROTEIN DETERMINATION; PROTEIN FUNCTION; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; STEM CELL; VALIDATION PROCESS; DNA MUTATIONAL ANALYSIS; GENE LOCUS; GENETICS; HIGH THROUGHPUT SCREENING; MUTATION; PROCEDURES; RNA EDITING;

CRISPR-CAS SYSTEMS; DNA MUTATIONAL ANALYSIS; GENETIC ENGINEERING; GENETIC LOCI; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MUTATION; POLYMERASE CHAIN REACTION; RNA EDITING;

EID: 84977260192     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0153901     Document Type: Article

References (28)

1. Joung JK, Sander JD. TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol. 2012; 14: 49-55. doi: 10.1038/nrm3486 PMID: 23169466
2. Sun N, Zhao H. Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing. Biotechnol Bioeng. 2013. doi: 10.1002/bit.24890
3. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013; 8: 2281-2308. doi: 10.1038/nprot.2013.143 PMID: 24157548
4. Doudna JA, Charpentier E. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014; 346: 1258096-1258096. doi: 10.1126/science.1258096 PMID: 25430774
5. Kim Y, Kweon J, Kim J-S. TALENs and ZFNs are associated with different mutation signatures. Nat Meth. 2013; 10: 185. doi: 10.1038/nmeth.2364
6. Sung YH, Kim JM, Kim HT, Lee J, Jeon J, Jin Y, et al. Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases. Genome Res. 2014; 24: 125-131. doi: 10.1101/gr.163394.113 PMID: 24253447
7. Flemr M, Bühler M. Single-Step Generation of Conditional Knockout Mouse Embryonic Stem Cells. Cell Reports. 2015; 12: 709-716. doi: 10.1016/j.celrep.2015.06.051 PMID: 26190102
8. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. American Association for the Advancement of Science; 2014; 343: 84-87. doi: 10.1126/science.1247005
9. Yang Z, Steentoft C, Hauge C, Hansen L, Thomsen AL, Niola F, et al. Fast and sensitive detection of indels induced by precise gene targeting. Nucleic Acids Research. 2015; 43: e59-e59. doi: 10.1093/ nar/gkv126 PMID: 25753669
10. Yu C, Zhang Y, Yao S, Wei Y. A PCR Based Protocol for Detecting Indel Mutations Induced by TALENs and CRISPR/Cas9 in Zebrafish. Jennings B, editor. PLoS ONE. 2014; 9: e98282-7. doi: 10.1371/ journal.pone.0098282 PMID: 24901507
11. Hendel A, Fine EJ, Bao G, Porteus MH. Quantifying on- and off-target genome editing. Trends Biotechnol. 2015; 33: 132-140. doi: 10.1016/j.tibtech.2014.12.001 PMID: 25595557
12. Wang K, Mei DY, Liu QN, Qiao XH, Ruan WM, Huang T, et al. Research of methods to detect genomic mutations induced by CRISPR/Cas systems. J Biotechnol. 2015; 214: 128-132. doi: 10.1016/j.jbiotec. 2015.09.029 PMID: 26419205
13. Vouillot L, Thélie A, Pollet N. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (Bethesda). 2015; 5: 407-415. doi: 10.1534/g3.114. 015834
14. Mock U, Machowicz R, Hauber I, Horn S, Abramowski P, Berdien B, et al. mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5. Nucleic Acids Research. 2015; 43: 5560-5571. doi: 10.1093/nar/gkv469 PMID: 25964300
15. Miyaoka Y, Chan AH, Judge LM, Yoo J, Huang M, Nguyen TD, et al. Isolation of single-base genomeedited human iPS cells without antibiotic selection. Nat Meth. 2014; 11: 291-293. doi: 10.1038/nmeth. 2840
16. Quail DF, Siegers GM, Jewer M, Postovit L-M. Nodal signalling in embryogenesis and tumourigenesis. The International Journal of Biochemistry & Cell Biology. 2013. doi: 10.1016/j.biocel.2012.12.021
17. Surana R, Sikka S, Cai W, Shin EM, Warrier SR, Tan HJG, et al. Secreted frizzled related proteins: Implications in cancers. Biochim Biophys Acta. 2014; 1845: 53-65. doi: 10.1016/j.bbcan.2013.11.004 PMID: 24316024
18. Streubel J, Blücher C, Landgraf A, Boch J. TAL effector RVD specificities and efficiencies. Nature Biotechnology. 2012; 30: 593-595. doi: 10.1038/nbt.2304 PMID: 22781676
19. Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, et al. Breaking the code of DNA binding specificity of TAL-type III effectors. Science. 2009; 326: 1509-1512. doi: 10.1126/science.1178811 PMID: 19933107
20. Cong L, Zhou R, Kuo Y-C, Cunniff M, Zhang F. Comprehensive interrogation of natural TALE DNAbinding modules and transcriptional repressor domains. Nat Comms. 2012; 3: 968. doi: 10.1038/ ncomms1962
21. Bell CC, Magor GW, Gillinder KR, Perkins AC. A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing. BMC Genomics. 2014; 15: 1002. doi: 10.1186/1471-2164-15-1002 PMID: 25409780
22. Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, VanDyk JK, et al. TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Research. 2012; 40: W117-W122. doi: 10.1093/nar/gks608 PMID: 22693217
23. Cermak T, Doyle EL, Christian M, Wang L, Zhang Y, Schmidt C, et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Research. 2011; 39: e82-e82. doi: 10.1093/nar/gkr218 PMID: 21493687
24. Jankele R, Svoboda P. TAL effectors: tools for DNA Targeting. Briefings in Functional Genomics. 2014; 13: 409-419. doi: 10.1093/bfgp/elu013 PMID: 24907364
25. Welch DR, Bisi JE, Miller BE, Conaway D, Seftor EA, Yohem KH, et al. Characterization of a highly invasive and spontaneously metastatic human malignant melanoma cell line. Int J Cancer. 1991; 47: 227-237. PMID: 1671030
26. Frank S, Skryabin BV, Greber B. A modified TALEN-based system for robust generation of knock-out human pluripotent stem cell lines and disease models. BMC Genomics. 2013; 14: 773. doi: 10.1186/ 1471-2164-14-773 PMID: 24206569
27. Corbisier P, Pinheiro L, Mazoua S, Kortekaas A-M, Chung PYJ, Gerganova T, et al. DNA copy number concentration measured by digital and droplet digital quantitative PCR using certified reference materials. Anal Bioanal Chem. 2015; 407: 1831-1840. doi: 10.1007/s00216-015-8458-z PMID: 25600685
28. Lin Y, Cradick TJ, Bao G. Designing and Testing the Activities of TAL Effector Nucleases. In: Storici F, editor. Gene Correction. Totowa, NJ: Humana Press; 2014. pp. 203-219. doi: 10.1007/978-1-62703-761-7-13