Identification of genome edited cells using CRISPRnano

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Genome engineering relies on DNA repair pathways like non-homologous end joining (NHEJ) and homology-directed repair (HDR).
• Identifying genetically modified clones accurately is a significant challenge in molecular biology research.
• Existing bioinformatics tools often require high-quality sequencing data, limiting their use with newer, portable sequencing technologies.

Purpose of the Study:

• To develop a versatile and user-friendly computational tool for analyzing genome engineering outcomes.
• To enable the analysis of low-quality sequencing reads from affordable, portable sequencers like Oxford Nanopore Technologies (ONT).
• To provide fast and accurate identification, quantification, and visualization of genetically modified cell lines.

Main Methods:

• Development of a computational webserver, CRISPRnano (www.CRISPRnano.de).
• The tool is designed to process both Next Generation Sequencing (NGS) and ONT sequencing reads.
• CRISPRnano offers offline functionality for enhanced accessibility.

Main Results:

• CRISPRnano successfully analyzes low-quality reads from portable sequencing devices.
• The webserver enables rapid and precise detection and quantification of targeted mutagenesis.
• It provides visualization of genetic modifications in engineered cell lines.

Conclusions:

• CRISPRnano offers a robust solution for analyzing genome engineering edits, particularly with data from portable sequencers.
• The tool democratizes the analysis of targeted mutagenesis by supporting low-quality reads.
• CRISPRnano enhances the efficiency and accessibility of genetic modification validation.