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

Methods and Protocols, vol. 8, pp. 23

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.

Authors 6

1. Bing Yao

   Utrecht University · University Medical Center Utrecht

   Affiliation as printed

   Experimental Cardiology Laboratory, Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

   Regenerative Medicine Center Utrecht, Circulatory Health Research Center, University Medical Center Utrecht, University Utrecht, 3584 CT Utrecht, The Netherlands

2. Qiangbing Yang

   University Medical Center Utrecht

   Affiliation as printed

   CDL Research, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

   Experimental Cardiology Laboratory, Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

3. Manuel A.F.V. Gonçalves Aachen Department of Cell and Chemical Biology

   Leiden University · Leiden University Medical Center

   Affiliation as printed

   Department of Cell and Chemical Biology, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands

4. Raymond Michel Schiffelers

   University Medical Center Utrecht

   Affiliation as printed

   CDL Research, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

5. Joost P. G. Sluijter

   Utrecht University · University Medical Center Utrecht

   Affiliation as printed

   Experimental Cardiology Laboratory, Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

   Regenerative Medicine Center Utrecht, Circulatory Health Research Center, University Medical Center Utrecht, University Utrecht, 3584 CT Utrecht, The Netherlands

6. Zhiyong Lei corresponding

   Utrecht University · University Medical Center Utrecht

   Affiliation as printed

   CDL Research, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

   Experimental Cardiology Laboratory, Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands

   Regenerative Medicine Center Utrecht, Circulatory Health Research Center, University Medical Center Utrecht, University Utrecht, 3584 CT Utrecht, The Netherlands