{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T18:08:42Z","timestamp":1780078122897,"version":"3.54.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T00:00:00Z","timestamp":1728432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-024-06959-z","type":"journal-article","created":{"date-parts":[[2024,10,9]],"date-time":"2024-10-09T22:02:00Z","timestamp":1728511320000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Gene editing of NCF1 loci is associated with homologous recombination and chromosomal rearrangements"],"prefix":"10.1038","volume":"7","author":[{"given":"Federica","family":"Raimondi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4609-9096","authenticated-orcid":false,"given":"Kah Mun","family":"Siow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominik","family":"Wrona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4209-7248","authenticated-orcid":false,"given":"Carla","family":"Fuster-Garc\u00eda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oleksandr","family":"Pastukhov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3216-7350","authenticated-orcid":false,"given":"Michael","family":"Schmitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katja","family":"Bargsten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4989-0695","authenticated-orcid":false,"given":"Lucas","family":"Kissling","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4412-9191","authenticated-orcid":false,"given":"Daan C.","family":"Swarts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5389-9481","authenticated-orcid":false,"given":"Geoffroy","family":"Andrieux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7757-4630","authenticated-orcid":false,"given":"Toni","family":"Cathomen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ute","family":"Modlich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7601-210X","authenticated-orcid":false,"given":"Martin","family":"Jinek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2458-2629","authenticated-orcid":false,"given":"Ulrich","family":"Siler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9008-1312","authenticated-orcid":false,"given":"Janine","family":"Reichenbach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,10,9]]},"reference":[{"key":"6959_CR1","doi-asserted-by":"publisher","first-page":"2619","DOI":"10.1182\/blood-2009-05-221606","volume":"114","author":"M Bianchi","year":"2009","unstructured":"Bianchi, M. et al. Restoration of NET formation by gene therapy in CGD controls aspergillosis. Blood 114, 2619\u20132622 (2009).","journal-title":"Blood"},{"key":"6959_CR2","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1089\/hgtb.2012.157","volume":"24","author":"C Brendel","year":"2013","unstructured":"Brendel, C. et al. Human miR223 promoter as a novel myelo-specific promoter for chronic granulomatous disease gene therapy. Hum. Gene Ther. Methods 24, 151\u2013159 (2013).","journal-title":"Hum. Gene Ther. Methods"},{"key":"6959_CR3","doi-asserted-by":"publisher","first-page":"416","DOI":"10.2174\/1566523215666150515145255","volume":"15","author":"U Siler","year":"2015","unstructured":"Siler, U. et al. Successful combination of sequential gene therapy and rescue Allo-HSCT in two children with X-CGD - importance of timing. Curr. Gene Ther. 15, 416\u2013427 (2015).","journal-title":"Curr. Gene Ther."},{"key":"6959_CR4","doi-asserted-by":"publisher","first-page":"936","DOI":"10.1016\/j.omtm.2020.04.015","volume":"17","author":"D Wrona","year":"2020","unstructured":"Wrona, D. et al. CRISPR-directed therapeutic correction at the NCF1 locus is challenged by frequent incidence of chromosomal deletions. Mol. Ther. Methods Clin. Dev. 17, 936\u2013943 (2020).","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"6959_CR5","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1016\/j.stemcr.2019.08.008","volume":"13","author":"D Klatt","year":"2019","unstructured":"Klatt, D. et al. Targeted repair of p47-CGD in iPSCs by CRISPR\/Cas9: functional correction without cleavage in the highly homologous pseudogenes. Stem Cell Reports 13, 590\u2013598 (2019).","journal-title":"Stem Cell Reports"},{"key":"6959_CR6","doi-asserted-by":"publisher","unstructured":"Schejtman, A. et al. Lentiviral gene therapy rescues p47phox chronic granulomatous disease and the ability to fight Salmonella infection in mice. Gene Ther. https:\/\/doi.org\/10.1038\/s41434-020-0164-6 (2020).","DOI":"10.1038\/s41434-020-0164-6"},{"key":"6959_CR7","doi-asserted-by":"publisher","first-page":"1662","DOI":"10.1016\/j.bbadis.2013.05.001","volume":"1832","author":"A Hayrapetyan","year":"2013","unstructured":"Hayrapetyan, A., Dencher, P. C. D., van Leeuwen, K., de Boer, M. & Roos, D. Different unequal cross-over events between NCF1 and its pseudogenes in autosomal p47(phox)-deficient chronic granulomatous disease. Biochim. Biophys. Acta 1832, 1662\u20131672 (2013).","journal-title":"Biochim. Biophys. Acta"},{"key":"6959_CR8","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1182\/bloodadvances.2016001214","volume":"1","author":"RK Merling","year":"2017","unstructured":"Merling, R. K. et al. Gene-edited pseudogene resurrection corrects p47phox-deficient chronic granulomatous disease. Blood Adv. 1, 270\u2013278 (2017).","journal-title":"Blood Adv."},{"key":"6959_CR9","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1038\/nbt.4192","volume":"36","author":"M Kosicki","year":"2018","unstructured":"Kosicki, M., Tomberg, K. & Bradley, A. Repair of double-strand breaks induced by CRISPR\u2013Cas9 leads to large deletions and complex rearrangements. Nat. Biotechnol. 36, 765\u2013771 (2018).","journal-title":"Nat. Biotechnol."},{"key":"6959_CR10","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09006-2","volume":"10","author":"G Cullot","year":"2019","unstructured":"Cullot, G. et al. CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations. Nat. Commun. 10, 1136 (2019).","journal-title":"Nat. Commun."},{"key":"6959_CR11","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1101\/gr.171322.113","volume":"24","author":"S Kim","year":"2014","unstructured":"Kim, S., Kim, D., Cho, S. W., Kim, J. & Kim, J.-S. Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res. 24, 1012\u20131019 (2014).","journal-title":"Genome Res."},{"key":"6959_CR12","doi-asserted-by":"publisher","unstructured":"Liang, X. et al. Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection. J. Biotechnol. https:\/\/doi.org\/10.1016\/j.jbiotec.2015.04.024 (2015).","DOI":"10.1016\/j.jbiotec.2015.04.024"},{"key":"6959_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-29332-2","volume":"13","author":"DM Sapozhnikov","year":"2023","unstructured":"Sapozhnikov, D. M. & Szyf, M. The PROTECTOR strategy employs dCas orthologs to sterically shield off-target sites from CRISPR\/Cas activity. Sci. Rep. 13, 2280 (2023).","journal-title":"Sci. Rep."},{"key":"6959_CR14","doi-asserted-by":"publisher","unstructured":"Ran, F. A. et al. Double nicking by RNA-guided CRISPR cas9 for enhanced genome editing specificity. Cell. https:\/\/doi.org\/10.1016\/j.cell.2013.08.021 (2013).","DOI":"10.1016\/j.cell.2013.08.021"},{"key":"6959_CR15","doi-asserted-by":"publisher","first-page":"1195","DOI":"10.1016\/j.celrep.2019.12.064","volume":"30","author":"T Hyodo","year":"2020","unstructured":"Hyodo, T. et al. Tandem paired nicking promotes precise genome editing with scarce interference by p53. Cell Rep. 30, 1195\u20131207.e7 (2020).","journal-title":"Cell Rep."},{"key":"6959_CR16","doi-asserted-by":"crossref","unstructured":"Swarts, D. C. & Jinek, M. Cas9 versus Cas12a\/Cpf1: structure\u2013function comparisons and implications for genome editing. Wiley Interdiscip. Rev. RNA 9, e148 (2018).","DOI":"10.1002\/wrna.1481"},{"key":"6959_CR17","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1038\/srep44187","volume":"7","author":"D Wrona","year":"2017","unstructured":"Wrona, D., Siler, U. & Reichenbach, J. CRISPR\/Cas9-generated p47 phox -deficient cell line for chronic granulomatous disease gene therapy vector development. Sci. Rep. 7, 6\u201311 (2017).","journal-title":"Sci. Rep."},{"key":"6959_CR18","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1016\/j.omtm.2019.02.001","volume":"13","author":"D Wrona","year":"2019","unstructured":"Wrona, D., Siler, U. & Reichenbach, J. Novel Diagnostic Tool for p47 phox -deficient chronic granulomatous disease patient and carrier detection. Mol. Ther. Methods Clin. Dev. 13, 274\u2013278 (2019).","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"6959_CR19","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/nrm.2016.177","volume":"18","author":"PM Deh\u00e9","year":"2017","unstructured":"Deh\u00e9, P. M. & Gaillard, P. H. L. Control of structure-specific endonucleases to maintain genome stability. Nat. Rev. Mol. Cell Biol. 18, 315\u2013330 (2017).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"6959_CR20","doi-asserted-by":"publisher","first-page":"6962","DOI":"10.1093\/nar\/gky588","volume":"46","author":"N Maizels","year":"2018","unstructured":"Maizels, N. & Davis, L. Initiation of homologous recombination at DNA nicks. Nucleic Acids Res. 46, 6962\u20136973 (2018).","journal-title":"Nucleic Acids Res."},{"key":"6959_CR21","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1038\/s41580-019-0152-0","volume":"20","author":"R Scully","year":"2019","unstructured":"Scully, R., Panday, A., Elango, R. & Willis, N. A. DNA double-strand break repair-pathway choice in somatic mammalian cells. Nat. Rev. Mol. Cell Biol. 20, 698\u2013714 (2019).","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"6959_CR22","doi-asserted-by":"publisher","first-page":"2800","DOI":"10.1073\/pnas.1720962115","volume":"115","author":"AK Ling","year":"2018","unstructured":"Ling, A. K. et al. Double-stranded DNA break polarity skews repair pathway choice during intrachromosomal and interchromosomal recombination. Proc. Natl. Acad. Sci. USA. 115, 2800\u20132805 (2018).","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"6959_CR23","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nmeth.2857","volume":"11","author":"B Shen","year":"2014","unstructured":"Shen, B. et al. Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat. Methods 11, 399\u2013402 (2014).","journal-title":"Nat. Methods"},{"key":"6959_CR24","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1038\/nrg2380","volume":"9","author":"KW Caldecott","year":"2008","unstructured":"Caldecott, K. W. Single-strand break repair and genetic disease. Nat. Rev. Genet. 9, 619\u2013631 (2008).","journal-title":"Nat. Rev. Genet."},{"key":"6959_CR25","doi-asserted-by":"publisher","unstructured":"Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. https:\/\/doi.org\/10.1126\/science.1225829 (2012).","DOI":"10.1126\/science.1225829"},{"key":"6959_CR26","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1038\/nbt.2675","volume":"31","author":"P Mali","year":"2013","unstructured":"Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833\u2013838 (2013).","journal-title":"Nat. Biotechnol."},{"key":"6959_CR27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-25190-6","volume":"12","author":"J Boutin","year":"2021","unstructured":"Boutin, J. et al. CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells. Nat. Commun. 12, 1\u201312 (2021).","journal-title":"Nat. Commun."},{"key":"6959_CR28","doi-asserted-by":"publisher","first-page":"2556","DOI":"10.1074\/jbc.A114.564625","volume":"292","author":"MC Canver","year":"2017","unstructured":"Canver, M. C. et al. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced short palindromic repeats (CRISPR)\/Cas9 nuclease system in mammalian cells. J. Biol. Chem. 292, 2556 (2017).","journal-title":"J. Biol. Chem."},{"key":"6959_CR29","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1016\/j.celrep.2015.01.016","volume":"10","author":"K Kraft","year":"2015","unstructured":"Kraft, K. et al. Deletions, inversions, duplications: engineering of structural variants using CRISPR\/Cas in mice. Cell Rep 10, 833\u2013839 (2015).","journal-title":"Cell Rep"},{"key":"6959_CR30","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.1016\/j.stem.2021.02.002","volume":"28","author":"G Turchiano","year":"2021","unstructured":"Turchiano, G. et al. Quantitative evaluation of chromosomal rearrangements in gene-edited human stem cells by CAST-Seq. Cell Stem Cell 28, 1136\u20131147.e5 (2021).","journal-title":"Cell Stem Cell"},{"key":"6959_CR31","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1086\/376565","volume":"73","author":"M Bay\u00e9s","year":"2003","unstructured":"Bay\u00e9s, M., Magano, L. F., Rivera, N., Flores, R. & P\u00e9rez Jurado, L. A. Mutational mechanisms of williams-beuren syndrome deletions. Am. J. Hum. Genet. 73, 131\u2013151 (2003).","journal-title":"Am. J. Hum. Genet."},{"key":"6959_CR32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1017\/S146239940700035X","volume":"9","author":"LR Osborne","year":"2007","unstructured":"Osborne, L. R. & Mervis, C. B. Rearrangements of the Williams\u2013Beuren syndrome locus: molecular basis and implications for speech and language development. Expert Rev. Mol. Med. 9, 1 (2007).","journal-title":"Expert Rev. Mol. Med."},{"key":"6959_CR33","doi-asserted-by":"crossref","unstructured":"Kimura, R. et al. Williams\u2013Beuren syndrome as a potential risk factor for burkitt lymphoma. Front. Genet. 9, 368 (2018).","DOI":"10.3389\/fgene.2018.00368"},{"key":"6959_CR34","doi-asserted-by":"publisher","unstructured":"Decimi, V. et al. Williams syndrome and mature B-Leukemia: a random association? Eur. J. Med. Genet. https:\/\/doi.org\/10.1016\/j.ejmg.2016.10.007 (2016).","DOI":"10.1016\/j.ejmg.2016.10.007"},{"key":"6959_CR35","doi-asserted-by":"publisher","first-page":"3955","DOI":"10.1111\/jcmm.13675","volume":"22","author":"Y Liu","year":"2018","unstructured":"Liu, Y. et al. LncRNA ABHD11-AS1 promotes the development of endometrial carcinoma by targeting cyclin D1. J. Cell. Mol. Med. 22, 3955\u20133964 (2018).","journal-title":"J. Cell. Mol. Med."},{"key":"6959_CR36","doi-asserted-by":"crossref","unstructured":"Wu, D. D. et al. Role of the lncRNA ABHD11-AS1 in the tumorigenesis and progression of epithelial ovarian cancer through targeted regulation of RhoC. Mol. Cancer 16, 138 (2017).","DOI":"10.1186\/s12943-017-0709-5"},{"key":"6959_CR37","first-page":"1343","volume":"8","author":"Y Li","year":"2018","unstructured":"Li, Y. et al. Multifaceted regulation and functions of replication factor C family in human cancers. Am. J. Cancer Res. 8, 1343 (2018).","journal-title":"Am. J. Cancer Res."},{"key":"6959_CR38","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.ejmg.2009.02.006","volume":"52","author":"V N","year":"2009","unstructured":"N, V. et al. Fourteen new cases contribute to the characterization of the 7q11.23 microduplication syndrome. Eur. J. Med. Genet. 52, 94\u2013100 (2009).","journal-title":"Eur. J. Med. Genet."},{"key":"6959_CR39","doi-asserted-by":"publisher","first-page":"6109","DOI":"10.1182\/blood-2011-12-397620","volume":"119","author":"A Jerez","year":"2012","unstructured":"Jerez, A. et al. Loss of heterozygosity in 7q myeloid disorders: clinical associations and genomic pathogenesis. Blood 119, 6109 (2012).","journal-title":"Blood"},{"key":"6959_CR40","doi-asserted-by":"publisher","first-page":"1348","DOI":"10.1038\/leu.2014.25","volume":"28","author":"N Hosono","year":"2014","unstructured":"Hosono, N. et al. Recurrent genetic defects on chromosome 7q in myeloid neoplasms. Leukemia 28, 1348 (2014).","journal-title":"Leukemia"},{"key":"6959_CR41","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/nrg.2015.25","volume":"17","author":"CMB Carvalho","year":"2016","unstructured":"Carvalho, C. M. B. & Lupski, J. R. Mechanisms underlying structural variant formation in genomic disorders. Nat. Rev. Genet. 17, 224 (2016).","journal-title":"Nat. Rev. Genet."},{"key":"6959_CR42","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2156-11-13","volume":"11","author":"T Brunson","year":"2010","unstructured":"Brunson, T., Wang, Q., Chambers, I. & Song, Q. A copy number variation in human NCF1 and its pseudogenes. BMC Genet. 11, 13 (2010).","journal-title":"BMC Genet."},{"key":"6959_CR43","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/j.gde.2013.05.007","volume":"23","author":"A Malkova","year":"2013","unstructured":"Malkova, A. & Ira, G. Break-induced replication: functions and molecular mechanism. Curr. Opin. Genet. Dev. 23, 271\u2013279 (2013).","journal-title":"Curr. Opin. Genet. Dev."},{"key":"6959_CR44","doi-asserted-by":"publisher","first-page":"88","DOI":"10.1126\/science.1243211","volume":"343","author":"L Costantino","year":"2014","unstructured":"Costantino, L. et al. Break-induced replication repair of damaged forks induces genomic duplications in human cells. Science 343, 88 (2014).","journal-title":"Science"},{"key":"6959_CR45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-020-15053-x","volume":"11","author":"NS McCarty","year":"2020","unstructured":"McCarty, N. S., Graham, A. E., Studen\u00e1, L. & Ledesma-Amaro, R. Multiplexed CRISPR technologies for gene editing and transcriptional regulation. Nat. Commun. 11, 1\u201313 (2020).","journal-title":"Nat. Commun."},{"key":"6959_CR46","doi-asserted-by":"publisher","DOI":"10.1016\/j.omtn.2024.102229","volume":"35","author":"KM Siow","year":"2024","unstructured":"Siow, K. M. et al. Targeted knock-in of NCF1 cDNA into the NCF2 locus leads to myeloid phenotypic correction of p47 phox -deficient chronic granulomatous disease. Mol. Ther. Nucleic Acids 35, 102229 (2024).","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"6959_CR47","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1038\/nbt.3513","volume":"34","author":"SS De Ravin","year":"2016","unstructured":"De Ravin, S. S. et al. Targeted gene addition in human CD34+ hematopoietic cells for correction of X-linked chronic granulomatous disease. Nat. Biotechnol. 34, 424\u2013429 (2016).","journal-title":"Nat. Biotechnol."},{"key":"6959_CR48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-78450-8","volume":"10","author":"H Hayashi","year":"2020","unstructured":"Hayashi, H., Kubo, Y., Izumida, M. & Matsuyama, T. Efficient viral delivery of Cas9 into human safe harbor. Sci. Rep. 10, 1\u201314 (2020).","journal-title":"Sci. Rep."},{"key":"6959_CR49","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/s41586-019-1711-4","volume":"576","author":"AV Anzalone","year":"2019","unstructured":"Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149\u2013157 (2019).","journal-title":"Nature"},{"key":"6959_CR50","doi-asserted-by":"publisher","first-page":"7129","DOI":"10.1182\/blood-2023-186365","volume":"142","author":"JM Heath","year":"2023","unstructured":"Heath, J. M. et al. Prime editing efficiently and precisely corrects causative mutation in chronic granulomatous disease, restoring myeloid function: toward development of a prime edited autologous hematopoietic stem cell therapy. Blood 142, 7129\u20137129 (2023).","journal-title":"Blood"},{"key":"6959_CR51","doi-asserted-by":"publisher","unstructured":"Fiumara, M. et al. Genotoxic effects of base and prime editing in human hematopoietic stem cells. Nat. Biotechnol. https:\/\/doi.org\/10.1038\/s41587-023-01915-4 (2023).","DOI":"10.1038\/s41587-023-01915-4"},{"key":"6959_CR52","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.jaci.2015.11.028","volume":"138","author":"M Weisser","year":"2016","unstructured":"Weisser, M. et al. Hyperinflammation in patients with chronic granulomatous disease leads to impairment of hematopoietic stem cell functions. J. Allergy Clin. Immunol. 138, 219\u2013228.e9 (2016).","journal-title":"J. Allergy Clin. Immunol."},{"key":"6959_CR53","doi-asserted-by":"publisher","first-page":"2059","DOI":"10.1101\/gr.177220.114","volume":"24","author":"P Essletzbichler","year":"2014","unstructured":"Essletzbichler, P. et al. Megabase-scale deletion using CRISPR\/Cas9 to generate a fully haploid human cell line. Genome Res. 24, 2059\u20132065 (2014).","journal-title":"Genome Res."},{"key":"6959_CR54","unstructured":"High-performance long-read assay enables contiguous data with N50 of 6\u20137 kb on existing Illumina platforms. Genomics Research Hub. Available at: https:\/\/www.illumina.com\/science\/genomics-research\/articles\/infinity-high-performance-long-read-assay.html (2022)."},{"key":"6959_CR55","unstructured":"The HiFi difference \u2014 true long reads vs synthetic long reads. Products, Procedures + Protocols. Available at: https:\/\/www.pacb.com\/blog\/the-hifi-difference-true-long-reads-vs-synthetic-long-reads\/. (2022)."},{"key":"6959_CR56","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1038\/ng753","volume":"29","author":"LR Osborne","year":"2001","unstructured":"Osborne, L. R. et al. A 1.5 million-base pair inversion polymorphism in families with Williams-Beuren syndrome. Nat. Genet. 29, 321\u2013325 (2001).","journal-title":"Nat. Genet."},{"key":"6959_CR57","doi-asserted-by":"publisher","first-page":"697","DOI":"10.1101\/gr.215095.116","volume":"27","author":"MH Weissensteiner","year":"2017","unstructured":"Weissensteiner, M. H. et al. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res. 27, 697\u2013708 (2017).","journal-title":"Genome Res."},{"key":"6959_CR58","doi-asserted-by":"publisher","unstructured":"Bothmer, A. et al. Characterization of the interplay between DNA repair and CRISPR\/Cas9-induced DNA lesions at an endogenous locus. Nat. Commun. https:\/\/doi.org\/10.1038\/ncomms13905 (2017).","DOI":"10.1038\/ncomms13905"},{"key":"6959_CR59","doi-asserted-by":"publisher","first-page":"588","DOI":"10.1038\/s41434-021-00271-9","volume":"28","author":"LI Schwarze","year":"2021","unstructured":"Schwarze, L. I., G\u0142\u00f3w, D., Sonntag, T., Uhde, A. & Fehse, B. Optimisation of a TALE nuclease targeting the HIV co-receptor CCR5 for clinical application. Gene Ther. 28, 588\u2013601 (2021).","journal-title":"Gene Ther."},{"key":"6959_CR60","doi-asserted-by":"publisher","first-page":"W171","DOI":"10.1093\/nar\/gkz365","volume":"47","author":"K Labun","year":"2019","unstructured":"Labun, K. et al. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 47, W171\u2013W174 (2019).","journal-title":"Nucleic Acids Res."},{"key":"6959_CR61","doi-asserted-by":"publisher","DOI":"10.1126\/science.1247997","volume":"343","author":"M Jinek","year":"2014","unstructured":"Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014).","journal-title":"Science"},{"key":"6959_CR62","doi-asserted-by":"publisher","unstructured":"Kissling, L., Monfort, A., Swarts, D. C., Wutz, A. & Jinek, M. Preparation and electroporation of Cas12a\/Cpf1-guide RNA complexes for introducing large gene deletions in mouse embryonic stem cells. Methods Enzymol. 616, 241\u2013263. https:\/\/doi.org\/10.1016\/bs.mie.2018.10.028 (2019).","DOI":"10.1016\/bs.mie.2018.10.028"},{"key":"6959_CR63","doi-asserted-by":"publisher","first-page":"e2842","DOI":"10.21769\/BioProtoc.2842","volume":"8","author":"P Mohanraju","year":"2018","unstructured":"Mohanraju, P., Van Der Oost, J., Jinek, M. & Swarts, D. C. Heterologous expression and purification of CRISPR-Cas12a\/Cpf1. Bio Protoc. 8, e2842 (2018).","journal-title":"Bio Protoc."},{"key":"6959_CR64","doi-asserted-by":"publisher","unstructured":"Brinkman, E. K. & van Steensel, B. Rapid quantitative evaluation of CRISPR genome editing by TIDE and TIDER. Methods Mol. Biol. https:\/\/doi.org\/10.1007\/978-1-4939-9170-9_3 (2019).","DOI":"10.1007\/978-1-4939-9170-9_3"},{"key":"6959_CR65","doi-asserted-by":"publisher","unstructured":"Klermund, J. et al. On- and off-target effects of paired CRISPR-Cas nickase in primary human cells. Mol. Ther. https:\/\/doi.org\/10.1016\/j.ymthe.2024.03.006 (2024).","DOI":"10.1016\/j.ymthe.2024.03.006"},{"key":"6959_CR66","doi-asserted-by":"publisher","first-page":"1130736","DOI":"10.3389\/fgeed.2023.1130736","volume":"5","author":"M Rhiel","year":"2023","unstructured":"Rhiel, M. et al. T-CAST: an optimized CAST-Seq pipeline for TALEN confirms superior safety and efficacy of obligate-heterodimeric scaffolds. Front.Genome Ed. 5, 1130736 (2023).","journal-title":"Front.Genome Ed."}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-024-06959-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-024-06959-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-024-06959-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,10]],"date-time":"2024-10-10T14:11:32Z","timestamp":1728569492000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-024-06959-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,9]]},"references-count":66,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["6959"],"URL":"https:\/\/doi.org\/10.1038\/s42003-024-06959-z","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,10,9]]},"assertion":[{"value":"30 September 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 September 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 October 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"1291"}}