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Legacy assays such as Sanger and short-read next-generation sequencing often fail to resolve complex structures including adeno-associated virus (AAV) inverted terminal repeats, lentiviral recombination, and mRNA poly(A) tails. Oxford Nanopore Technologies enables long-read, native single-molecule sequencing to access these attributes directly. This review summarizes nanopore sequencing across the CGT lifecycle. For plasmid DNA, it confirms full-length circular identity and reveals structural heterogeneity missed by restriction mapping. For viral vectors (AAV and lentivirus), it functions as an integrity assay to distinguish full genomes from truncations and to detect sequence-resolved impurities, including reverse-packaged plasmid backbones. For mRNA therapeutics, direct RNA sequencing profiles poly(A) tail length distributions and base modifications (\n                    <jats:italic toggle=\"yes\">e.g.,<\/jats:italic>\n                    m\n                    <jats:sup>1<\/jats:sup>\n                    \u03a8) in a single assay. We also discuss adaptive sampling for impurity enrichment and native epigenetic profiling of bacterial methylation. Finally, we assess limitations in accuracy and compliance and outline the regulatory path toward moving long-read sequencing from an orthogonal tool to a validated lot-release method. Overall, nanopore sequencing supports risk-based, high-resolution QC while reducing analytical turnaround time.\n                  <\/jats:p>","DOI":"10.1177\/10430342261454725","type":"journal-article","created":{"date-parts":[[2026,6,13]],"date-time":"2026-06-13T05:23:17Z","timestamp":1781328197000},"page":"991-1007","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":0,"title":["Resolving the Unresolvable: Nanopore Sequencing as a Comprehensive Quality Control Platform for Gene Therapy Vectors"],"prefix":"10.1177","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4523-4439","authenticated-orcid":false,"given":"Yan","family":"Xu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology &amp; Blood Diseases Hospital, Chinese Academy of Medical Sciences &amp; Peking Union Medical College, Tianjin, China"},{"name":"Tianjin Institutes of Health Science, Tianjin, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Bing","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology &amp; Blood Diseases Hospital, Chinese Academy of Medical Sciences &amp; Peking Union Medical College, Tianjin, China"},{"name":"Tianjin Institutes of Health Science, Tianjin, China."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian-Ping","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology &amp; Blood Diseases Hospital, Chinese Academy of Medical Sciences &amp; Peking Union Medical College, Tianjin, China"},{"name":"Tianjin Institutes of Health Science, Tianjin, China."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"179","published-online":{"date-parts":[[2026,6,12]]},"reference":[{"key":"e_1_3_2_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymthe.2023.11.001"},{"key":"e_1_3_2_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-19505-2"},{"key":"e_1_3_2_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan4672"},{"key":"e_1_3_2_5_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aar6711"},{"key":"e_1_3_2_6_1","unstructured":"5.American Society of Gene & Cell Therapy and Citeline. 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