Skip to main content Accessibility help
×
Hostname: page-component-848d4c4894-2pzkn Total loading time: 0 Render date: 2024-06-03T23:37:06.381Z Has data issue: false hasContentIssue false

12 - Detection of Insertion/Deletion (Indel) Events after Genome Targeting: Pros and Cons of the Available Methods

from Part III - Technology Development and Screening

Published online by Cambridge University Press:  30 July 2018

Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
Get access

Summary

Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Chapter
Information
Genome Editing and Engineering
From TALENs, ZFNs and CRISPRs to Molecular Surgery
, pp. 181 - 194
Publisher: Cambridge University Press
Print publication year: 2018

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Bae, S, Kweon, J, Kim, HS, Kim, J-S. 2014. Microhomology-based choice of Cas9 nuclease target sites. Nat Methods 11(7): 705706.CrossRefGoogle ScholarPubMed
Beumer, KJ, Trautman, JK, Christian, M, et al. 2013. Comparing zinc finger nucleases and transcription activator-like effector nucleases for gene targeting in Drosophila. G3 (Bethesda) 3(10): 17171725.CrossRefGoogle ScholarPubMed
Bibikova, M, Carroll, D, Segal, DJ, et al. 2001. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21(1): 289297.CrossRefGoogle ScholarPubMed
Brinkman, EK, Chen, T, Amendola, M, van Steensel, B. 2014. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res 42(22): e168.CrossRefGoogle ScholarPubMed
Børresen, AL, Hovig, E, Brøgger, A. 1988. Detection of base mutations in genomic DNA using denaturing gradient gel electrophoresis (DGGE) followed by transfer and hybridization with gene-specific probes. Mutation Res 202(1): 7783.CrossRefGoogle ScholarPubMed
Chen, F, Pruett-Miller, SM, Huang, Y, et al. 2011. High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases. Nat Methods 8(9): 753755.CrossRefGoogle ScholarPubMed
Chen, S, Oikonomou, G, Chiu, CN, et al. 2013. A large-scale in vivo analysis reveals that TALENs are significantly more mutagenic than ZFNs generated using context-dependent assembly. Nucleic Acids Res 41(4): 27692778.CrossRefGoogle ScholarPubMed
Cong, L, Ran, FA, Cox, D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339(6121): 819823.CrossRefGoogle ScholarPubMed
Dahlem, TJ, Hoshijima, K, Jurynec, MJ, et al. 2012. Simple methods for generating and detecting locus-specific mutations induced with TALENs in the zebrafish genome. PLoS Genet 8(8): e1002861.CrossRefGoogle ScholarPubMed
Deriano, L, Roth, DB. 2013. Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu Rev Genet 47: 433455.CrossRefGoogle ScholarPubMed
Doench, JG, Fusi, N, Sullender, M, et al. 2016. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34: 112.CrossRefGoogle ScholarPubMed
Doench, JG, Hartenian, E, Graham, DB, et al. 2014. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 32(12): 12621267.CrossRefGoogle ScholarPubMed
Eshaghpour, H, Crothers, DM. 1978. Preparative separation of the complementary strands of DNA restriction fragments by alkaline RPC-5 chromatography. Nucleic Acids Res 5(5): 16271637.CrossRefGoogle ScholarPubMed
Foley, JE, Maeder, ML, Pearlberg, J, et al. 2009. Targeted mutagenesis in zebrafish using customized zinc-finger nucleases. Nat Protocols 4(12): 18551867.CrossRefGoogle ScholarPubMed
Fu, Y, Foden, JA, Khayter, C, et al. 2013. High-frequency off-target mutagenesis induced by CrIsPr-Cas nucleases in human cells. Nat Biotechnol 31(9): 822826.CrossRefGoogle ScholarPubMed
Gao, H, Huang, J, Barany, F, Cao, W. 2007. Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations. Nucleic Acids Res 35(1): 16.Google ScholarPubMed
Geurts, AM, Cost, GJ, Freyvert, Y, et al. 2010. Knockout rats produced using designed zinc finger nucleases. Science 325(5939): 20092011.Google Scholar
Güell, M, Yang, L, Church, G. 2014. Genome editing assessment using CRISPR genome analyzer. Bioinformatics 30(20): 29682970.CrossRefGoogle ScholarPubMed
Huang, MC, Cheong, WC, Lim, LS, Li, M-H. 2012. A simple, high sensitivity mutation screening using Ampligase mediated T7 endonuclease I and Surveyor nuclease with microfluidic capillary electrophoresis. Electrophoresis 33(5): 788796.CrossRefGoogle ScholarPubMed
Inazuka, M, Wenz, H, Sakabe, M, Tahira, T, Hayashi, K. 1997. A streamlined mutation detection system: multicolor post-PCR fluorescence labeling and single-strand conformational polymorphism analysis by capillary electrophoresis. Genome Res 7(11): 10941103.CrossRefGoogle ScholarPubMed
Jinek, M, East, A, Cheng, A, et al. 2013. RNA-programmed genome editing in human cells. eLife 2(3): e00471.CrossRefGoogle ScholarPubMed
Kim, HH, Um, E, Cho, S, Jung, C, Kim, J. 2011. Surrogate reporters for enrichment of cells with nuclease-induced mutations. Nat Methods 8(11): 941943.CrossRefGoogle ScholarPubMed
Kim, Y, Kweon, J, Kim, J-S. 2013. TALENs and ZFNs are associated with different mutation signatures. Nat Methods 10(3): 185.CrossRefGoogle ScholarPubMed
Kosicki, M, Rajan, SS, Lorenzetti, FC, et al. 2017. Dynamics of indel profiles induced by various CRISPR/Cas9 delivery methods. Prog Mol Biol Trans Sci 152: 4967.CrossRefGoogle ScholarPubMed
Kuan, SF, Byrd, JC, Basbaum, C, Kim, YS. 1989. Inhibition of mucin glycosylation by aryl-N-acetyl-alpha-galactosaminides in human colon cancer cells. J Biol Chem 264(32): 1927119277.CrossRefGoogle ScholarPubMed
Lindsay, H, Burger, A, Biyong, B, et al. 2015. CrispR variants: precisely charting the mutation spectrum in genome engineering experiments. Nat Biotechnol 34(7): 701703.CrossRefGoogle Scholar
Liu, W, Smith, DI, Rechtzigel, KJ, Thibodeau, SN, James, CD. 2002. Denaturing high performance liquid chromatography (DHPLC) used in the detection of germline and somatic mutations. Nucleic Acids Res 26(6): 13961400.CrossRefGoogle Scholar
Liu, X, Homma, A, Sayadi, J, et al. 2016. Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system. Sci Rep 6: 19675.CrossRefGoogle ScholarPubMed
Lonowski, LA, Narimatsu, Y, Riaz, A, et al. 2017. Genome editing using FACS enrichment of nuclease expressing cells and Indel Detection by Amplicon Analysis (IDAA). Nat Protoc 12(3): 581603.CrossRefGoogle Scholar
Mali, P, Yang, L, Esvelt, KM, et al. 2013. RNA-guided human genome engineering via Cas9. Science 339(6121): 823826.CrossRefGoogle ScholarPubMed
Mashal, RD, Koontz, J, Sklar, J. 1995. Detection of mutations by cleavage of DNA heteroduplexes with bacteriophage resolvases. Nat Genet 2: 177183.CrossRefGoogle Scholar
Miller, JC, Holmes, MC, Wang, J, et al. 2007. An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25(7): 778785.CrossRefGoogle ScholarPubMed
Moscou, MJ, Bogdanove, AJ. 2009. A simple cipher governs DNA recognition by TAL effectors. Science 326(5959): 1501.CrossRefGoogle ScholarPubMed
Nakade, S, Tsubota, T, Sakane, Y, et al. 2014. Microhomology-mediated end-joining-dependent integration of donor DNA in cells and animals using TALENs and CRISPR/Cas9. Nat Comm 5: 5560.CrossRefGoogle ScholarPubMed
Oleykowski, CA, Mullins, CRB, Godwin, AK, Yeung, AT. 1998. Mutation detection using a novel plant endonuclease. Nucleic Acids Res 26(20): 45974602.CrossRefGoogle ScholarPubMed
Pimkin, M, Caretti, E, Canutescu, A, et al. 2007. Recombinant nucleases CEL I from celery and SP I from spinach for mutation detection. BMC Biotechnol 7: 29.CrossRefGoogle Scholar
Pinello, L, Canver, MC, Hoban, MD, et al. 2016. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotech 34(7): 695697.CrossRefGoogle ScholarPubMed
Qiu, P, Shandilya, H, D’Alessio, JM, et al. 2004. Mutation detection using Surveyor nuclease. BioTechniques 36(4): 702707.CrossRefGoogle ScholarPubMed
Sakurai, T, Watanabe, S, Kamiyoshi, A, Sato, M, Shindo, T. 2014. A single blastocyst assay optimized for detecting CRISPR/Cas9 system-induced indel mutations in mice. BMC Biotechnol 14(1): 69.CrossRefGoogle ScholarPubMed
Shalem, O, Sanjana, NE, Hartenian, E, et al. 2013. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343(6166): 8487.CrossRefGoogle ScholarPubMed
Smith, GR. 2004. How homologous recombination is initiated: unexpected evidence for single-strand nicks from v(d)j site-specific recombination. Cell 117(2): 146148.CrossRefGoogle ScholarPubMed
Smith, J, Berg, JM, Chandrasegaran, S. 1999. A detailed study of the substrate specificity of a chimeric restriction enzyme. Nucleic Acids Res 27(2): 674681.CrossRefGoogle ScholarPubMed
Smith, J, Bibikova, M, Whitby, FG, et al. 2000. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 28(17): 33613369.CrossRefGoogle ScholarPubMed
Stark, JM, Pierce, AJ, Oh, J, Pastink, A, Jasin, M. 2004. Genetic steps of mammalian homologous repair with distinct mutagenic consequences. Mol Cell Biol 24(21): 93059316.CrossRefGoogle ScholarPubMed
Symington, LS, Gautier, J. 2011. Double-strand break end resection and repair pathway choice. Annu Rev Genet 45: 247273.CrossRefGoogle ScholarPubMed
Urnov, FD, Miller, JC, Lee, YL, et al. 2005. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435(7042): 646651.CrossRefGoogle ScholarPubMed
Van Overbeek, M, Capurso, D, Carter, MM, et al. 2016. DNA repair profiling reveals nonrandom outcomes at Cas9-mediated breaks. Molecular Cell 63: 114.Google ScholarPubMed
Vouillot, L, Thelie, A, Pollet, N. 2015. Comparison of T7E1 and surveyor mismatch cleavage assays to detect mutations triggered by engineered nucleases. G3 (Bethesda) 5(3): 407415.CrossRefGoogle ScholarPubMed
Yang, L, Guell, M, Byrne, S, et al. 2013. Optimization of scarless human stem cell genome editing. Nucleic Acids Res 41(19): 90499061.CrossRefGoogle ScholarPubMed
Yang, Z, Steentoft, C, Hauge, C, et al. 2015. Fast and sensitive detection of indels induced by precise gene targeting. Nucleic Acids Res 43(9): e59.CrossRefGoogle ScholarPubMed
Yeung, AT, Hattangadi, D, Blakesley, L, Nicolas, E. 2005. Enzymatic mutation detection technologies. BioTechniques 38(5): 749758.CrossRefGoogle ScholarPubMed
Youil, R, Kemper, BW, Cotton, RG. 1995. Screening for mutations by enzyme mismatch cleavage with T4 endonuclease VII. Proc Natl Acad Sci USA 92(1): 8791.CrossRefGoogle ScholarPubMed
Yu, C, Zhang, Y, Yao, S, Wei, Y. 2014. A PCR based protocol for detecting indel mutations induced by TALENs and CRISPR/Cas9 in zebrafish. PLoS One 9(6): e98282.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×