{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T13:56:02Z","timestamp":1791035762987,"version":"4.1.0"},"reference-count":34,"publisher":"SAGE Publications","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license"}],"content-domain":{"domain":["journals.sagepub.com"],"crossmark-restriction":true},"short-container-title":["The CRISPR Journal"],"abstract":"<jats:p>Advances in CRISPR-Cas9-based genome editing have simplified the generation of isogenic induced pluripotent stem cell (iPSC) pairs differing by a single genetic perturbation, minimizing interindividual variability in disease modeling. However, imprecise editing can cause unintended mutations that distort genotype-phenotype interpretation. Here, we investigated the molecular consequences of CRISPR-Cas9 editing in human iPSCs carrying a tandem duplication of the STAG2 locus. Using hybridization capture-based targeted next-generation sequencing of genomic regions surrounding Cas9-induced double-strand breaks, we identified inversions, plasmid DNA integrations, and complex structural rearrangements that had been missed by conventional PCR-based genotyping. The main advance of our study is the application of a practical hybridization capture-based workflow for resolving such hidden editing outcomes during the generation of isogenic iPSC models. In the selected clones subjected to detailed analysis, targeted sequencing enabled us to revise the initial interpretation of editing outcomes and resolve discrepancies between genotypic and transcriptomic data. Our results demonstrate that complex on-target alterations can remain undetected by conventional PCR-based genotyping and show that hybridization capture-based targeted sequencing can serve as a practical quality-control approach for the characterization of edited iPSC clones.<\/jats:p>","DOI":"10.1177\/25731599261492640","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:05:13Z","timestamp":1790834713000},"update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Hidden Outcomes of CRISPR-Cas9 Genome Editing Revealed by Targeted Sequencing in Isogenic Human iPSC Clones"],"prefix":"10.1177","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-1894-9458","authenticated-orcid":false,"given":"Maria","family":"Tubalova","sequence":"first","affiliation":[{"name":"Institute of Cytology and Genetics, Novosibirsk, Russia."},{"name":"Novosibirsk State University, Novosibirsk, Russia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Galina","family":"Koksharova","sequence":"additional","affiliation":[{"name":"Sirius University of Science and Technology, Sochi, Russia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Silvia Souza da","family":"Costa","sequence":"additional","affiliation":[{"name":"Department of Genetics and Evolutionary Biology, Human Genome Research Center, Institute of Biosciences, University of S\u00e3o Paulo, S\u00e3o Paulo, SP, Brazil."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana Cristina Victorino","family":"Krepischi","sequence":"additional","affiliation":[{"name":"Department of Genetics and Evolutionary Biology, Human Genome Research Center, Institute of Biosciences, University of S\u00e3o Paulo, S\u00e3o Paulo, SP, Brazil."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veniamin","family":"Fishman","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics, Novosibirsk, Russia."},{"name":"Novosibirsk State University, Novosibirsk, Russia."},{"name":"Sirius University of Science and Technology, Sochi, Russia."},{"name":"Artificial Intelligence Research Institute, Novosibirsk, Russia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Gridina","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics, Novosibirsk, Russia."},{"name":"Novosibirsk State University, Novosibirsk, Russia."},{"name":"Sirius University of Science and Technology, Sochi, Russia."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"e_1_3_6_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/jcmm.14916"},{"key":"e_1_3_6_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-09006-2"},{"key":"e_1_3_6_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4192"},{"key":"e_1_3_6_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-018-0380-z"},{"key":"e_1_3_6_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms21103604"},{"key":"e_1_3_6_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-025-07539-5"},{"key":"e_1_3_6_8_1","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.abo7676"},{"key":"e_1_3_6_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.stemcr.2022.02.008"},{"key":"e_1_3_6_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107689"},{"key":"e_1_3_6_11_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab686"},{"key":"e_1_3_6_12_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-10050-6"},{"key":"e_1_3_6_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.scr.2025.103785"},{"key":"e_1_3_6_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.scr.2025.103781"},{"key":"e_1_3_6_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s13577-025-01193-z"},{"key":"e_1_3_6_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbadis.2024.167569"},{"key":"e_1_3_6_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.scr.2025.103857"},{"key":"e_1_3_6_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/cge.12567"},{"key":"e_1_3_6_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddv414"},{"key":"e_1_3_6_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2013.143"},{"key":"e_1_3_6_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2019.06.022"},{"key":"e_1_3_6_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41366-022-01149-5"},{"key":"e_1_3_6_23_1","doi-asserted-by":"publisher","DOI":"10.3390\/diagnostics11040708"},{"key":"e_1_3_6_24_1","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2020.00616"},{"key":"e_1_3_6_25_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1000327"},{"key":"e_1_3_6_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddp306"},{"key":"e_1_3_6_27_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1008924"},{"key":"e_1_3_6_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz459"},{"key":"e_1_3_6_29_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aag3260"},{"key":"e_1_3_6_30_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.04.004"},{"key":"e_1_3_6_31_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00439-023-02561-1"},{"key":"e_1_3_6_32_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jgg.2019.11.002"},{"key":"e_1_3_6_33_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymthe.2023.01.004"},{"key":"e_1_3_6_34_1","article-title":"Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy","author":"Jia MS","year":"2025","unstructured":"33.Jia MS, , Padmaswari MH, , Burcham LA, et al. Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy. bioRxiv 2025.","journal-title":"bioRxiv"},{"key":"e_1_3_6_35_1","doi-asserted-by":"crossref","unstructured":"34.H\u00f6ijer I van Schendel R Emmanouilidou A et al. Accurate characterization of CRISPR-Cas9 genome editing outcomes and mosaicism with near-perfect long reads. 2025; 2025.09.08.674810.","DOI":"10.1101\/2025.09.08.674810"}],"container-title":["The CRISPR Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/25731599261492640","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/full-xml\/10.1177\/25731599261492640","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.sagepub.com\/doi\/pdf\/10.1177\/25731599261492640","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T13:48:11Z","timestamp":1791035291000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.sagepub.com\/doi\/10.1177\/25731599261492640"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":34,"alternative-id":["10.1177\/25731599261492640"],"URL":"https:\/\/doi.org\/10.1177\/25731599261492640","relation":{},"ISSN":["2573-1599","2573-1602"],"issn-type":[{"value":"2573-1599","type":"print"},{"value":"2573-1602","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]},"article-number":"25731599261492640"}}