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Updated: Apr 16, 2026

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
Published on: November 1, 2024
Fast and sensitive detection of indels induced by precise gene targeting
Zhang Yang1, Catharina Steentoft2, Camilla Hauge3
1Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark.
We developed Indel Detection by Amplicon Analysis (IDAA), a fast and sensitive method for detecting small DNA insertions and deletions (indels) after gene editing. This technique accurately measures indel sizes for high-throughput genomic analysis.
Area of Science:
- Genomics
- Molecular Biology
- Biotechnology
Background:
- Nuclease-based gene editing tools enable precise genome alteration.
- Detecting small insertions and deletions (indels) induced by gene editing is challenging with traditional methods.
- Efficient detection of indels is crucial for high-throughput genomic studies.
Purpose of the Study:
- To develop a fast, sensitive, and simple method for detecting and characterizing DNA indels.
- To accurately determine indel sizes down to ±1 bp.
- To provide a high-throughput compatible assay for gene editing analysis.
Main Methods:
- Indel Detection by Amplicon Analysis (IDAA) utilizes tri-primer amplicon labeling.
- DNA capillary electrophoresis is employed for detection.
- The method is designed for high-throughput applications.
Main Results:
- IDAA provides fast and sensitive indel detection.
- The method accurately defines indel sizes with ±1 bp resolution.
- IDAA is suitable for high-throughput analysis of gene editing outcomes.
Conclusions:
- IDAA offers a significant improvement for detecting gene editing-induced indels.
- This method addresses a key limitation in precise genome engineering.
- IDAA facilitates efficient and accurate characterization of DNA modifications.
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