INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing

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

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  • 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.
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