nanoGET · Nanopore based evaluation of genomic, epigenetic and transcriptomic impact of gene editing

Genome editing technologies such as CRISPR/Cas9 have transformed biomedical research and hold great therapeutic promise. Current safety evaluation strategies focus primarily on genomic alterations—off-target mutations, large deletions, and chromosomal rearrangements while largely overlooking transcriptomic and epigenomic consequences. Moreover, safety profiling is fragmented across multiple platforms, limiting accessibility and routine implementation. This project, nanoGET, will establish a comprehensive, single-platform pipeline for safety evaluation of genome editing using nanopore sequencing which uniquely enables long-read sequencing of both DNA and RNA while simultaneously detecting base modifications, allowing integrated analysis of genomic, transcriptomic, and epigenetic changes within a single workflow. The pipeline will benchmark ONT against gold-standard methods for off-target detection, large deletions, DNA methylation profiling, chromatin accessibility, and transcriptomics. Using human iPSCs, the project will systematically evaluate the consequences of editing across the three layers. A key innovation is the direct comparison of double-strand break (DSB)-mediated editors (Cas9) with DSB-free approaches (base and prime editors), generating the first integrated dataset to quantify multi-layered differences between editing modalities. By delivering an affordable, scalable, and standardized pipeline, nanoGET will provide novel insights into unintended consequences of editing, enable rational selection of editing methods, and accelerate the development of safer therapeutic strategies. Beyond research impact, this platform will expand access to high-quality safety evaluation worldwide, strengthening scientific progress, innovation, and public trust in genome editing.