Comparative analysis of methods for assessing on-target gene editing efficiencies

Yao, B.; Yang, Q.B.; Goncalves, M.A.F.V.; Schiffelers, R.; Sluijter, J.P.G.; Lei, Z.Y. (2025)

Article / Letter to editor

Genome editing based on CRISPR-derived technologies has become a cornerstone in both fundamental research and clinical applications. Accurately measuring editing efficiency is crucial for developing and applying genome editing strategies. This study offers a detailed comparison of widely used techniques for evaluating on-target gene editing efficiency, including T7 Endonuclease I (T7EI), Tracking of Indels by Decomposition (TIDE), Inference of CRISPR Edits (ICE), droplet digital PCR (ddPCR), and live-cell assays involving engineered fluorescent reporter cells. Through a comparative analysis, this study highlights the unique strengths and limitations of each method, aiding researchers in choosing the most appropriate method for their specific needs, ensuring more tailored monitoring of genome editing outcomes in a precise and reliable manner.

• genome editing
• CRISPR/Cas9
• editing efficiency
• on-target gene editing
• genome editing assays

• All authors: Yao, B.; Yang, Q.B.; Goncalves, M.A.F.V.; Schiffelers, R.; Sluijter, J.P.G.; Lei, Z.Y.
• Date: 2025-03-01
• Journal: Methods and Protocols
• Volume: 8
• Issue: 2
• DOI: doi:10.3390/mps8020023