{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T23:27:24Z","timestamp":1786663644014,"version":"build-2736575974"},"reference-count":45,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,8,14]],"date-time":"2026-08-14T00:00:00Z","timestamp":1786665600000},"content-version":"vor","delay-in-days":84,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82402188"],"award-info":[{"award-number":["82402188"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Commun Biol"],"DOI":"10.1038\/s42003-026-10298-6","type":"journal-article","created":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T16:25:47Z","timestamp":1779467147000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["AviTag-seq unifies nucleotide-resolution maps of CRISPR off-targets and AAV vector integrations"],"prefix":"10.1038","volume":"9","author":[{"given":"Jia-Xin","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0228-3203","authenticated-orcid":false,"given":"Shu-Man","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Yu","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-7565-1860","authenticated-orcid":false,"given":"Dong-Hao","family":"Deng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei-Dong","family":"Bai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan-Juan","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An","family":"Gong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shan-Chen","family":"Pang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4360-6718","authenticated-orcid":false,"given":"Shu-Dong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5194-5077","authenticated-orcid":false,"given":"Jian-Ping","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4319-6181","authenticated-orcid":false,"given":"Xiao-Bing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,22]]},"reference":[{"key":"10298_CR1","doi-asserted-by":"publisher","first-page":"3283","DOI":"10.1182\/blood-2013-04-497354","volume":"122","author":"XM Anguela","year":"2013","unstructured":"Anguela, X. M. et al. Robust ZFN-mediated genome editing in adult hemophilic mice. Blood 122, 3283\u20133287 (2013).","journal-title":"Blood"},{"key":"10298_CR2","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1038\/s41591-019-0344-3","volume":"25","author":"CE Nelson","year":"2019","unstructured":"Nelson, C. E. et al. Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. Nat. Med. 25, 427\u2013432 (2019).","journal-title":"Nat. Med."},{"key":"10298_CR3","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1089\/hum.2019.037","volume":"30","author":"L Liu","year":"2019","unstructured":"Liu, L. et al. In vivo exon replacement in the mouse Atp7b gene by the Cas9 system. Hum. Gene Ther. 30, 1079\u20131092 (2019).","journal-title":"Hum. Gene Ther."},{"key":"10298_CR4","doi-asserted-by":"publisher","first-page":"6082","DOI":"10.1167\/iovs.17-21902","volume":"58","author":"W Wu","year":"2017","unstructured":"Wu, W. et al. AAV-CRISPR\/Cas9-mediated depletion of VEGFR2 blocks angiogenesis in vitro. Invest. Ophthalmol. Vis. Sci. 58, 6082\u20136090 (2017).","journal-title":"Invest. Ophthalmol. Vis. Sci."},{"key":"10298_CR5","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/j.omtm.2023.07.009","volume":"30","author":"L Xu","year":"2023","unstructured":"Xu, L. et al. Molecular dynamics of genome editing with CRISPR-Cas9 and rAAV6 virus in human HSPCs to treat sickle cell disease. Mol. Ther. Methods Clin. Dev. 30, 317\u2013331 (2023).","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"10298_CR6","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":"10298_CR7","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1038\/nature24644","volume":"551","author":"NM Gaudelli","year":"2017","unstructured":"Gaudelli, N. M. et al. Programmable base editing of A\u2022T to G\u2022C in genomic DNA without DNA cleavage. Nature 551, 464\u2013471 (2017).","journal-title":"Nature"},{"key":"10298_CR8","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1038\/s41586-020-1978-5","volume":"578","author":"JA Doudna","year":"2020","unstructured":"Doudna, J. A. The promise and challenge of therapeutic genome editing. Nature 578, 229\u2013236 (2020).","journal-title":"Nature"},{"key":"10298_CR9","doi-asserted-by":"publisher","first-page":"2646","DOI":"10.1016\/j.ymthe.2022.06.004","volume":"30","author":"DE Sabatino","year":"2022","unstructured":"Sabatino, D. E. et al. Evaluating the state of the science for adeno-associated virus integration: an integrated perspective. Mol. Ther. 30, 2646\u20132663 (2022).","journal-title":"Mol. Ther."},{"key":"10298_CR10","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1038\/nbt.3117","volume":"33","author":"SQ Tsai","year":"2015","unstructured":"Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat. Biotechnol. 33, 187\u2013197 (2015).","journal-title":"Nat. Biotechnol."},{"key":"10298_CR11","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1038\/s42003-024-06360-w","volume":"7","author":"Z-X Yang","year":"2024","unstructured":"Yang, Z.-X. et al. OliTag-seq enhances in cellulo detection of CRISPR-Cas9 off-targets. Commun. Biol. 7, 696 (2024).","journal-title":"Commun. Biol."},{"key":"10298_CR12","doi-asserted-by":"publisher","first-page":"1380","DOI":"10.1016\/j.cell.2013.08.021","volume":"154","author":"FA Ran","year":"2013","unstructured":"Ran, F. A. et al. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154, 1380\u20131389 (2013).","journal-title":"Cell"},{"key":"10298_CR13","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1038\/s41587-020-0555-7","volume":"38","author":"CR Lazzarotto","year":"2020","unstructured":"Lazzarotto, C. R. et al. CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity. Nat. Biotechnol. 38, 1317\u20131327 (2020).","journal-title":"Nat. Biotechnol."},{"key":"10298_CR14","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1038\/ng.3389","volume":"47","author":"J-C Nault","year":"2015","unstructured":"Nault, J.-C. et al. Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas. Nat. Genet. 47, 1187\u20131193 (2015).","journal-title":"Nat. Genet."},{"key":"10298_CR15","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1089\/hum.2017.009","volume":"28","author":"RJ Chandler","year":"2017","unstructured":"Chandler, R. J., Sands, M. S. & Venditti, C. P. Recombinant adeno-associated viral integration and genotoxicity: insights from animal models. Hum. Gene Ther. 28, 314\u2013322 (2017).","journal-title":"Hum. Gene Ther."},{"key":"10298_CR16","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1126\/science.1142658","volume":"317","author":"A Donsante","year":"2007","unstructured":"Donsante, A. et al. AAV vector integration sites in mouse hepatocellular carcinoma. Science 317, 477 (2007).","journal-title":"Science"},{"key":"10298_CR17","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/j.jviromet.2013.01.004","volume":"189","author":"T Brady","year":"2013","unstructured":"Brady, T. et al. Quantitation of HIV DNA integration: effects of differential integration site distributions on Alu-PCR assays. J. Virol. Methods 189, 53\u201357 (2013).","journal-title":"J. Virol. Methods"},{"key":"10298_CR18","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1038\/nm.2057","volume":"15","author":"R Gabriel","year":"2009","unstructured":"Gabriel, R. et al. Comprehensive genomic access to vector integration in clinical gene therapy. Nat. Med. 15, 1431\u20131436 (2009).","journal-title":"Nat. Med."},{"key":"10298_CR19","doi-asserted-by":"publisher","first-page":"1379","DOI":"10.1038\/nprot.2010.87","volume":"5","author":"A Paruzynski","year":"2010","unstructured":"Paruzynski, A. et al. Genome-wide high-throughput integrome analyses by nrLAM-PCR and next-generation sequencing. Nat. Protoc. 5, 1379\u20131395 (2010).","journal-title":"Nat. Protoc."},{"key":"10298_CR20","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1038\/s41592-023-01840-z","volume":"20","author":"RS Zou","year":"2023","unstructured":"Zou, R. S. et al. Improving the sensitivity of in vivo CRISPR off-target detection with DISCOVER-Seq. Nat. Methods 20, 706\u2013713 (2023).","journal-title":"Nat. Methods"},{"key":"10298_CR21","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1126\/science.aav9023","volume":"364","author":"B Wienert","year":"2019","unstructured":"Wienert, B. et al. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 364, 286\u2013289 (2019).","journal-title":"Science"},{"key":"10298_CR22","doi-asserted-by":"publisher","first-page":"4998","DOI":"10.1128\/jvi.68.8.4998-5006.1994","volume":"68","author":"DM McCarty","year":"1994","unstructured":"McCarty, D. M., Ryan, J. H., Zolotukhin, S., Zhou, X. & Muzyczka, N. Interaction of the adeno-associated virus Rep protein with a sequence within the A palindrome of the viral terminal repeat. J. Virol. 68, 4998\u20135006 (1994).","journal-title":"J. Virol."},{"key":"10298_CR23","doi-asserted-by":"publisher","first-page":"9933","DOI":"10.1128\/JVI.79.15.9933-9944.2005","volume":"79","author":"J Grieger","year":"2005","unstructured":"Grieger, J. & Samulski, R. Packaging capacity of adeno-associated virus serotypes: impact of larger genomes on infectivity and postentry steps. J. Virol. 79, 9933\u20139944 (2005).","journal-title":"J. Virol."},{"key":"10298_CR24","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/mt.2009.255","volume":"18","author":"Z Wu","year":"2010","unstructured":"Wu, Z., Yang, H. & Colosi, P. Effect of genome size on AAV vector packaging. Mol. Ther. 18, 80\u201386 (2010).","journal-title":"Mol. Ther."},{"key":"10298_CR25","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1038\/nbt.3737","volume":"35","author":"B Zetsche","year":"2017","unstructured":"Zetsche, B. et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat. Biotechnol. 35, 31\u201334 (2017).","journal-title":"Nat. Biotechnol."},{"key":"10298_CR26","doi-asserted-by":"publisher","first-page":"863","DOI":"10.1038\/nbt.3609","volume":"34","author":"D Kim","year":"2016","unstructured":"Kim, D. et al. Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells. Nat. Biotechnol. 34, 863\u2013868 (2016).","journal-title":"Nat. Biotechnol."},{"key":"10298_CR27","doi-asserted-by":"publisher","DOI":"10.1097\/BS9.0000000000000217","volume":"7","author":"J-J Zhao","year":"2025","unstructured":"Zhao, J.-J. et al. Enhancing hemophilia A gene therapy by strategic F8 deletions in AAV vectors. Blood Sci 7, e00217 (2025).","journal-title":"Blood Sci"},{"key":"10298_CR28","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1907-9","volume":"20","author":"J-P Zhang","year":"2019","unstructured":"Zhang, J.-P. et al. Curing hemophilia A by NHEJ-mediated ectopic F8 insertion in the mouse. Genome Biol 20, 276 (2019).","journal-title":"Genome Biol"},{"key":"10298_CR29","doi-asserted-by":"publisher","first-page":"288","DOI":"10.1038\/s41575-022-00729-0","volume":"20","author":"N Zabaleta","year":"2023","unstructured":"Zabaleta, N., Unzu, C., Weber, N. D. & Gonzalez-Aseguinolaza, G. Gene therapy for liver diseases - progress and challenges. Nat. Rev. Gastroenterol. Hepatol. 20, 288\u2013305 (2023).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"10298_CR30","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1016\/j.ymthe.2020.12.007","volume":"29","author":"JR Mendell","year":"2021","unstructured":"Mendell, J. R. et al. Current clinical applications of in vivo gene therapy with AAVs. Mol. Ther. 29, 464\u2013488 (2021).","journal-title":"Mol. Ther."},{"key":"10298_CR31","doi-asserted-by":"publisher","first-page":"809118","DOI":"10.3389\/fmed.2021.809118","volume":"8","author":"HKE Au","year":"2022","unstructured":"Au, H. K. E., Isalan, M. & Mielcarek, M. Gene therapy advances: a meta-analysis of AAV usage in clinical settings. Front. Med. 8, 809118 (2022).","journal-title":"Front. Med."},{"key":"10298_CR32","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1038\/s41573-019-0012-9","volume":"18","author":"D Wang","year":"2019","unstructured":"Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358\u2013378 (2019).","journal-title":"Nat. Rev. Drug Discov."},{"key":"10298_CR33","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-12449-2","volume":"10","author":"KS Hanlon","year":"2019","unstructured":"Hanlon, K. S. et al. High levels of AAV vector integration into CRISPR-induced DNA breaks. Nat. Commun. 10, 4439 (2019).","journal-title":"Nat. Commun."},{"key":"10298_CR34","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1038\/ng1380","volume":"36","author":"DG Miller","year":"2004","unstructured":"Miller, D. G., Petek, L. M. & Russell, D. W. Adeno-associated virus vectors integrate at chromosome breakage sites. Nat. Genet. 36, 767\u2013773 (2004).","journal-title":"Nat. Genet."},{"key":"10298_CR35","doi-asserted-by":"publisher","first-page":"3550","DOI":"10.1128\/MCB.23.10.3550-3557.2003","volume":"23","author":"DG Miller","year":"2003","unstructured":"Miller, D. G., Petek, L. M. & Russell, D. W. Human gene targeting by adeno-associated virus vectors is enhanced by DNA double-strand breaks. Mol. Cell. Biol. 23, 3550\u20133557 (2003).","journal-title":"Mol. Cell. Biol."},{"key":"10298_CR36","doi-asserted-by":"publisher","first-page":"101365","DOI":"10.1016\/j.omtm.2024.101365","volume":"32","author":"K Singh","year":"2024","unstructured":"Singh, K., Fronza, R., Evens, H., Chuah, M. K. & VandenDriessche, T. Comprehensive analysis of off-target and on-target effects resulting from liver-directed CRISPR-Cas9-mediated gene targeting with AAV vectors. Mol. Ther. Methods Clin. Dev. 32, 101365 (2024).","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"10298_CR37","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1038\/nbt.2889","volume":"32","author":"X Wu","year":"2014","unstructured":"Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat. Biotechnol. 32, 670\u2013676 (2014).","journal-title":"Nat. Biotechnol."},{"key":"10298_CR38","doi-asserted-by":"publisher","first-page":"1892","DOI":"10.1002\/1873-3468.12707","volume":"591","author":"KT Jensen","year":"2017","unstructured":"Jensen, K. T. et al. Chromatin accessibility and guide sequence secondary structure affect CRISPR-Cas9 gene editing efficiency. FEBS Lett 591, 1892\u20131901 (2017).","journal-title":"FEBS Lett"},{"key":"10298_CR39","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1756-8935-7-33","volume":"7","author":"M Tsompana","year":"2014","unstructured":"Tsompana, M. & Buck, M. J. Chromatin accessibility: a window into the genome. Epigenet. Chromatin 7, 33 (2014).","journal-title":"Epigenet. Chromatin"},{"key":"10298_CR40","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/s41587-020-0741-7","volume":"39","author":"GN Nguyen","year":"2021","unstructured":"Nguyen, G. N. et al. A long-term study of AAV gene therapy in dogs with hemophilia A identifies clonal expansions of transduced liver cells. Nat. Biotechnol. 39, 47\u201355 (2021).","journal-title":"Nat. Biotechnol."},{"key":"10298_CR41","doi-asserted-by":"publisher","first-page":"lqab019","DOI":"10.1093\/nargab\/lqab019","volume":"3","author":"N Stoler","year":"2021","unstructured":"Stoler, N. & Nekrutenko, A. Sequencing error profiles of Illumina sequencing instruments. NAR Genomics Bioinforma 3, lqab019 (2021).","journal-title":"NAR Genomics Bioinforma"},{"key":"10298_CR42","doi-asserted-by":"publisher","first-page":"72","DOI":"10.1038\/nmeth.1778","volume":"9","author":"T Kivioja","year":"2012","unstructured":"Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72\u201374 (2012).","journal-title":"Nat. Methods"},{"key":"10298_CR43","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1093\/stmcls\/sxae056","volume":"42","author":"Y-D Sun","year":"2024","unstructured":"Sun, Y.-D. et al. A p21 reporter iPSC line for evaluating CRISPR-Cas9 and vector-induced stress responses. Stem Cells 42, 992\u20131005 (2024).","journal-title":"Stem Cells"},{"key":"10298_CR44","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":"10298_CR45","doi-asserted-by":"publisher","first-page":"113070","DOI":"10.1016\/j.jim.2021.113070","volume":"495","author":"Y Dong","year":"2021","unstructured":"Dong, Y., Bai, H., Dong, F., Zhang, X.-B. & Ema, H. Gene knockout in highly purified mouse hematopoietic stem cells by CRISPR\/Cas9 technology. J. Immunol. Methods 495, 113070 (2021).","journal-title":"J. Immunol. Methods"}],"container-title":["Communications Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10298-6","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10298-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10298-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,13]],"date-time":"2026-08-13T22:47:44Z","timestamp":1786661264000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s42003-026-10298-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,22]]},"references-count":45,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["10298"],"URL":"https:\/\/doi.org\/10.1038\/s42003-026-10298-6","relation":{},"ISSN":["2399-3642"],"issn-type":[{"value":"2399-3642","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,22]]},"assertion":[{"value":"10 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 May 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 May 2026","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","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"1101"}}