A new easy-to-use web server to identify genome-edited cells

Nucleic acid research (2022). DOI: 10.1093/nar/gkac440″ width=”481″ height=”325″/>

From input to output: fast and accurate identification, quantification and visualization of genome editing events using CRISPRnano. Credit: Nucleic acid research (2022). DOI: 10.1093/nar/gkac440

A team of scientists from the IUF-Leibniz Research Institute for Environmental Medicine in Düsseldorf have developed and validated a computer web server that allows scientists to genotype mutations using nanopore sequencing. The results of this study have been published in the journal Nucleic acid research.

Diseases of genetic origin can be studied by inducing the respective mutations in cell lines which are then used to model human diseases. The overall objective is to elucidate the underlying mechanisms, interactions with environmental factors and ideally to find curative strategies. A crucial step in generating models of genetically modified cells is to verify the inserted mutation. Therefore, the genetic information carrier of the cells is decoded (sequencing) and compared to the reference set of genetic information in healthy individuals (genotyping). To help scientists make the comparison, different workflows and software are available, but many of them require expensive high-level sequencers or manual curation efforts.

To solve this problem, a team of scientists from the Laboratory for Genome Engineering and Model Development at the IUF – Leibniz Research Institute for Environmental Medicine in Düsseldorf, led by Dr. Andrea Rossi, developed a robust computational tool , versatile and easy to use. web server named CRISPRnano that allows analysis of noisy playbacks generated by affordable and portable sequencers, including Oxford Nanopore Technologies (ONT) devices. CRISPRnano allows rapid and precise identification, quantification and visualization of genetically modified cell lines; it is compatible with next-generation sequencing (NGS) and ONT readouts, and it can be used without an internet connection.


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More information:
Thach Nguyen et al, Identification of genome-edited cells using CRISPRnano, Nucleic acid research (2022). DOI: 10.1093/nar/gkac440

Provided by Leibniz-Institut für umweltmedizinische Forschung

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