INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing
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- dc.contributor.author Ivančić, Dimitrije
- dc.contributor.author Mir-Pedrol, Júlia
- dc.contributor.author Jaraba-Wallace, Jessica
- dc.contributor.author Rafel i Fontanals, Núria, 1954-
- dc.contributor.author Sánchez-Mejías, Avencia
- dc.contributor.author Güell Cargol, Marc, 1982-
- dc.date.accessioned 2022-12-19T07:29:11Z
- dc.date.available 2022-12-19T07:29:11Z
- dc.date.issued 2022
- dc.description.abstract Comprehensive characterisation of genome engineering technologies is relevant for their development and safe use in human gene therapy. Short-read based methods can overlook insertion events in repetitive regions. We develop INSERT-seq, a method that combines targeted amplification of integrated DNA, UMI-based correction of PCR bias and Oxford Nanopore long-read sequencing for robust analysis of DNA integration. The experimental pipeline improves the number of mappable insertions at repetitive regions by 4.8-7.3% and larger repeats are processed with a computational peak calling pipeline. INSERT-seq is a simple, cheap and robust method to quantitatively characterise DNA integration in diverse ex vivo and in vivo samples.
- dc.description.sponsorship We thank funding received from UPGRADE (European Union Horizon 2020, grant agreement No 825825), Fundación Ramón Areces (“Advanced gene editing technologies to restore LAMA2 on merosin-deficient congenital muscular dystrophy type 1A”), MdM projecte de recerca “Unidad de Excelencia María de Maeztu”, funded by the AEI (CEX2018-000792-M).
- dc.format.mimetype application/pdf
- dc.identifier.citation Ivančić D, Mir-Pedrol J, Jaraba-Wallace J, Rafel N, Sanchez-Mejias A, Güell M. INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing. Genome Biol. 2022 Oct 25;23(1):227. DOI: 10.1186/s13059-022-02778-9
- dc.identifier.doi http://dx.doi.org/10.1186/s13059-022-02778-9
- dc.identifier.issn 1474-7596
- dc.identifier.uri http://hdl.handle.net/10230/55166
- dc.language.iso eng
- dc.publisher BioMed Central
- dc.relation.ispartof Genome Biol. 2022 Oct 25;23(1):227
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/825825
- dc.rights © The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.title INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion