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CRISPR/Cas9 Genome Editing

CRISPR/Cas9 Genome Editing

The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...

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Related Experiment Video

Updated: May 24, 2026

CIRCLE-Seq for Interrogation of Off-Target Gene Editing

CIRCLE-Seq for Interrogation of Off-Target Gene Editing

Published on: November 1, 2024

CleanFinder: a scalable framework for comprehensive genome editing analysis.

Haribaskar Ramachandran¹, Jochen Dobner², Thach Nguyen¹

¹Genome Engineering and Model Development Laboratory, IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.

Trends in Biotechnology

|May 22, 2026

Summary

This summary is machine-generated.

CleanFinder is a new software tool that analyzes complex genome editing results. It accurately genotypes diverse edits, enabling efficient high-throughput screening and analysis of genetic modifications.

Keywords:

CRISPR/Cas CleanFinder genome editing analysis genotyping long-read sequencing prime editing

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Area of Science:

Genetics
Bioinformatics
Molecular Biology

Background:

Genome editing frequently produces heterogeneous allelic mixtures, posing analytical challenges for diverse editing techniques and sequencing platforms.
Accurate genotyping of these complex edits is crucial for understanding editing outcomes and for applications like high-throughput screening.

Purpose of the Study:

To develop a flexible and scalable browser-native framework, CleanFinder, for comprehensive genotyping of genome editing outcomes.
To address the analytical challenges in resolving heterogeneous edits across various editing modalities and genomic contexts.

Main Methods:

Developed CleanFinder, a browser-native framework utilizing a constrained semi-global alignment strategy for genotyping.
Implemented context-aware alignment modes supporting indels, base substitutions, and prime editing modifications in nuclear and mitochondrial DNA.
Integrated optional turbo mode for high-throughput analysis and an allele-aware module for detecting allelic dropout using heterozygous SNPs.

Main Results:

CleanFinder efficiently processed a large dataset from a small-molecule screen (1849 compounds in HEK293T cells).
The framework enabled high-throughput comparison of genome editing outcomes and identification of candidate compounds.
Demonstrated scalability and practical performance for analyzing diverse editing scenarios.

Conclusions:

CleanFinder provides a robust and scalable platform for detailed genome editing analysis.
The software facilitates systematic comparison of editing outcomes across various edit types and genomic contexts.
Enables efficient analysis for applications such as high-throughput screening and discovery.