Landrum, M. J. et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980–D985 (2014).
Google Scholar
Cordaux, R. & Batzer, M. A. The impact of retrotransposons on human genome evolution. Nat. Rev. Genet. 10, 691–703 (2009).
Google Scholar
Chen, J. M., Stenson, P. D., Cooper, D. N. & Ferec, C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum. Genet. 117, 411–427 (2005).
Google Scholar
Hancks, D. C. & Kazazian, H. H. Roles for retrotransposon insertions in human disease. Mob. DNA 7, 9 (2016).
Google Scholar
Wang, L., Norris, E. T. & Jordan, I. K. Human retrotransposon insertion polymorphisms are associated with health and disease via gene regulatory phenotypes. Front. Microbiol. 8, 1418 (2017).
Google Scholar
Hancks, D. C. & Kazazian, H. H. Jr. Active human retrotransposons: variation and disease. Curr. Opin. Genet. Dev. 22, 191–203 (2012).
Google Scholar
Qian, Y. et al. Identification of pathogenic retrotransposon insertions in cancer predisposition genes. Cancer Genet. 216-217, 159–169 (2017).
Google Scholar
Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380–1389 (2013).
Google Scholar
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Google Scholar
Kato, T. et al. Creation of mutant mice with megabase-sized deletions containing custom-designed breakpoints by means of the CRISPR/Cas9 system. Sci. Rep. 7, 59 (2017).
Google Scholar
Hara, S. et al. Microinjection-based generation of mutant mice with a double mutation and a 0.5 Mb deletion in their genome by the CRISPR/Cas9 system. J. Reprod. Dev. 62, 531–536 (2016).
Google Scholar
Wang, L. et al. Large genomic fragment deletion and functional gene cassette knock-in via Cas9 protein mediated genome editing in one-cell rodent embryos. Sci. Rep. 5, 17517 (2015).
Google Scholar
Yeh, C. D., Richardson, C. D. & Corn, J. E. Advances in genome editing through control of DNA repair pathways. Nat. Cell Biol. 21, 1468–1478 (2019).
Google Scholar
Zheng, Q. et al. Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells. Biotechniques 57, 115–124 (2014).
Google Scholar
Cox, D. B., Platt, R. J. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat. Med. 21, 121–131 (2015).
Google Scholar
Liu, M. et al. Methodologies for improving HDR efficiency. Front. Genet. 9, 691 (2018).
Google Scholar
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
Google Scholar
Matsoukas, I. G. Prime editing: genome editing for rare genetic diseases without double-strand breaks or donor DNA. Front. Genet. 11, 528 (2020).
Google Scholar
Liu, P. et al. Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. Nat. Commun. 12, 2121 (2021).
Google Scholar
Jang, H. et al. Prime editing enables precise genome editing in mouse liver and retina. Preprint at bioRxiv https://doi.org/10.1101/2021.01.08.425835 (2021).
Schene, I. F. et al. Prime editing for functional repair in patient-derived disease models. Nat. Commun. 11, 5352 (2020).
Google Scholar
Jiang, Y. Y. et al. Prime editing efficiently generates W542L and S621I double mutations in two ALS genes in maize. Genome Biol. 21, 257 (2020).
Google Scholar
Song, X., Huang, H., Xiong, Z., Ai, L. & Yang, S. CRISPR–Cas9D10A nickase-assisted genome editing in Lactobacillus casei. Appl. Environ. Microbiol. 83, 1259–1275 (2017).
Google Scholar
Cho, S. W. et al. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res. 24, 132–141 (2014).
Google Scholar
Sfeir, A. & Symington, L. S. Microhomology-mediated end joining: a back-up survival mechanism or dedicated pathway? Trends Biochem. Sci 40, 701–714 (2015).
Google Scholar
Bhargava, R., Onyango, D. O. & Stark, J. M. Regulation of single-strand annealing and its role in genome maintenance. Trends Genet. 32, 566–575 (2016).
Google Scholar
Kim, H. K. et al. Predicting the efficiency of prime editing guide RNAs in human cells. Nat. Biotechnol. 39, 198–206 (2021).
Google Scholar
Mir, A. et al. Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing. Nat. Commun. 9, 2641 (2018).
Google Scholar
Certo, M. T. et al. Tracking genome engineering outcome at individual DNA breakpoints. Nat. Methods 8, 671–676 (2011).
Google Scholar
Zhan, H., Li, A., Cai, Z., Huang, W. & Liu, Y. Improving transgene expression and CRISPR–Cas9 efficiency with molecular engineering-based molecules. Clin. Transl Med. 10, e194 (2020).
Google Scholar
Chen, R. et al. Enrichment of transiently transfected mesangial cells by cell sorting after cotransfection with GFP. Am. J. Physiol. 276, F777–F785 (1999).
Google Scholar
Homann, S. et al. A novel rapid and reproducible flow cytometric method for optimization of transfection efficiency in cells. PLoS ONE 12, e0182941 (2017).
Google Scholar
Pham, C. T., MacIvor, D. M., Hug, B. A., Heusel, J. W. & Ley, T. J. Long-range disruption of gene expression by a selectable marker cassette. Proc. Natl Acad. Sci. USA 93, 13090–13095 (1996).
Google Scholar
Grompe, M. et al. Loss of fumarylacetoacetate hydrolase is responsible for the neonatal hepatic dysfunction phenotype of lethal albino mice. Genes Dev. 7, 2298–2307 (1993).
Google Scholar
Paulk, N. K. et al. Adeno-associated virus gene repair corrects a mouse model of hereditary tyrosinemia in vivo. Hepatology 51, 1200–1208 (2010).
Google Scholar
Choi, J. et al. Precise genomic deletions using paired prime editing. Nat. Biotechnol. https://doi.org/10.1038/s41587-021-01025-z (in the press).
VanLith, C. J. et al. Ex vivo hepatocyte reprograming promotes homology-directed DNA repair to correct metabolic disease in mice after transplantation. Hepatol. Commun. 3, 558–573 (2019).
Google Scholar
Dutta, A. et al. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res. 45, 2585–2599 (2016).
Google Scholar
Aida, T. et al. Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ. BMC Genomics 17, 979 (2016).
Google Scholar
Warby, S. C. et al. CAG expansion in the Huntington disease gene is associated with a specific and targetable predisposing haplogroup. Am. J. Hum. Genet. 84, 351–366 (2009).
Google Scholar
Wang, Y. et al. Identification of a Xist silencing domain by Tiling CRISPR. Sci. Rep. 9, 2408 (2019).
Google Scholar
He, W. et al. De novo identification of essential protein domains from CRISPR–Cas9 tiling-sgRNA knockout screens. Nat. Commun. 10, 4541 (2019).
Google Scholar
Xue, W. et al. Response and resistance to NF-κB inhibitors in mouse models of lung adenocarcinoma. Cancer Discov. 1, 236–247 (2011).
Google Scholar
Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Google Scholar
Clement, K. et al. CRISPResso2 provides accurate and rapid genome editing sequence analysis. Nat. Biotechnol. 37, 224–226 (2019).
Google Scholar
