Vaidyanathan, S., McCarra, M. & Desai, T. J. Lung stem cells and therapy for cystic fibrosis. In Lung Stem Cells in Development, Health and Disease (eds Nikolić, M. Z. & and Hoganheffield, B. L. M.) 306–321 (European Respiratory Society, 2021).

Itoh, M. et al. Footprint-free gene mutation correction in induced pluripotent stem cell (iPSC) derived from recessive dystrophic epidermolysis bullosa (RDEB) using the CRISPR/Cas9 and piggyBac transposon system. J. Dermatol. Sci. 98, 163–172 (2020).

Article  CAS  PubMed  Google Scholar 

Wilkinson, A. C. et al. Cas9-AAV6 gene correction of beta-globin in autologous HSCs improves sickle cell disease erythropoiesis in mice. Nat. Commun. 12, 686 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khalil, A. M. The genome editing revolution. J. Genet. Eng. Biotechnol. 18, 68 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Martin, R. M. et al. Highly efficient and marker-free genome editing of human pluripotent stem cells by CRISPR–Cas9 RNP and AAV6 donor-mediated homologous recombination. Cell Stem Cell 24, 821–828 (2019).

Article  CAS  PubMed  Google Scholar 

Dever, D. P. et al. CRISPR/Cas9 β-globin gene targeting in human haematopoietic stem cells. Nature 539, 384–389 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gaj, T. et al. Targeted gene knock-in by homology-directed genome editing using Cas9 ribonucleoprotein and AAV donor delivery. Nucleic Acids Res. 45, e98 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Charlesworth, C. T. et al. Priming human repopulating hematopoietic stem and progenitor cells for Cas9/sgRNA gene targeting. Mol. Ther. Nucleic Acids 12, 89–104 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Romero, Z. et al. Editing the sickle cell disease mutation in human hematopoietic stem cells: comparison of endonucleases and homologous donor templates. Mol. Ther. 27, 1389–1406 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zheng, Y. et al. Efficient in vivo homology-directed repair within cardiomyocytes. Circulation 145, 787–789 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Kuzmin, D. A. et al. The clinical landscape for AAV gene therapies. Nat. Rev. Drug Discov. 20, 173–175 (2021).

Article  CAS  PubMed  Google Scholar 

Hanlon, K. S. et al. High levels of AAV vector integration into CRISPR-induced DNA breaks. Nat. Commun. 10, 4439 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Nelson, C. E. et al. Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nat. Med. 25, 427–432 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koniali, L., Lederer, C. W. & Kleanthous, M. Therapy development by genome editing of hematopoietic stem cells. Cells 10, 1492 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haltalli, M. L. et al. Hematopoietic stem cell gene editing and expansion: state-of-the-art technologies and recent applications. Exp. Hemat. 107, 9–13 (2022).

Article  CAS  PubMed  Google Scholar 

Notta, F. et al. Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment. Science 333, 218–221 (2011).

Article  CAS  PubMed  Google Scholar 

Soldner, F. & Jaenisch, R. Stem cells, genome editing, and the path to translational medicine. Cell 175, 615–632 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moço, P. D., Aharony, N. & Kamen, A. Adeno‐associated viral vectors for homology‐directed generation of CAR‐T cells. Biotechnol. J. 15, 1900286 (2020).

Article  Google Scholar 

Bak, R. O. et al. Multiplexed genetic engineering of human hematopoietic stem and progenitor cells using CRISPR/Cas9 and AAV6. eLife 6, e27873 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Martin, R. M. et al. Improving the safety of human pluripotent stem cell therapies using genome-edited orthogonal safeguards. Nat. Commun. 11, 2713 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Straathof, K. C. et al. An inducible caspase 9 safety switch for T-cell therapy. Blood 105, 4247–4254 (2005).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haberman, R. P., McCown, T. J. & Samulski, R. J. Novel transcriptional regulatory signals in the adeno-associated virus terminal repeat A/D junction element. J. Virol. 74, 8732–8739 (2000).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Flotte, T. R. et al. Expression of the cystic fibrosis transmembrane conductance regulator from a novel adeno-associated virus promoter. J. Biol. Chem. 268, 3781–3790 (1993).

Article  CAS  PubMed  Google Scholar 

Bak, R. O., Dever, D. P. & Porteus, M. H. CRISPR/Cas9 genome editing in human hematopoietic stem cells. Nat. Protoc. 13, 358–376 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duan, D. et al. Circular intermediates of recombinant adeno-associated virus have defined structural characteristics responsible for long-term episomal persistence in muscle tissue. J. Virol. 72, 8568–8577 (1998).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shestak, A. G. et al. Allelic dropout is a common phenomenon that reduces the diagnostic yield of PCR-based sequencing of targeted gene panels. Front. Genet. 12, 62033721 (2021).

Kanagawa, T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96, 317–323 (2003).

Article  CAS  PubMed  Google Scholar 

McCarty, D. et al. Adeno-associated virus terminal repeat (TR) mutant generates self-complementary vectors to overcome the rate-limiting step to transduction in vivo. Gene Ther. 10, 2112–2118 (2003).

Article  CAS  PubMed  Google Scholar 

Ma, E. et al. Single-stranded DNA cleavage by divergent CRISPR–Cas9 enzymes. Mol. Cell 60, 398–407 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ferrari, S. et al. Choice of template delivery mitigates the genotoxic risk and adverse impact of editing in human hematopoietic stem cells. Cell Stem Cell 29, 1428–1444 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nishimura, T. et al. Sufficiency for inducible Caspase-9 safety switch in human pluripotent stem cells and disease cells. Gene Ther. 27, 525–534 (2020).

Article  CAS  Google Scholar 

Chao, M. P. et al. Human AML-iPSCs reacquire leukemic properties after differentiation and model clonal variation of disease. Cell Stem Cell 20, 329–344 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ang, L. T. et al. Generating human artery and vein cells from pluripotent stem cells highlights the arterial tropism of Nipah and Hendra viruses. Cell 185, 2523–2541 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Whale, A. S., Huggett, J. F. & Tzonev, S. Fundamentals of multiplexing with digital PCR. Biomol. Detect. Quantif. 10, 15–23 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar