Comparative Analysis of Methods for Assessing On-Target Gene Editing Efficiencies

Bing Yao; Qiangbing Yang; Manuel A F V Gonçalves; Raymond Schiffelers; Joost P G Sluijter; Zhiyong Lei

doi:10.3390/mps8020023

Comparative Analysis of Methods for Assessing On-Target Gene Editing Efficiencies

Bing Yao, Qiangbing Yang, Manuel A F V Gonçalves, Raymond Schiffelers, Joost P G Sluijter, Zhiyong Lei^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

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.

Original language	English
Article number	23
Number of pages	14
Journal	Methods and Protocols
Volume	8
Issue number	2
DOIs	https://doi.org/10.3390/mps8020023
Publication status	Published - 1 Mar 2025

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AU - Gonçalves, Manuel A F V

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AU - Sluijter, Joost P G

AU - Lei, Zhiyong

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AB - 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.

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Comparative Analysis of Methods for Assessing On-Target Gene Editing Efficiencies

Abstract

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