Tag Archives: Leibniz-Institut für umweltmedizinische Forschung (IUF)

What is CRISPRnano?

To answer the question, CRISPRnano is a computational webserver for identifying gene-edited cells. (For those unfamiliar with CRISPR, it stands for clustered regularly interspaced short palindromic repeats’ a form of gene editing,)

The webserver was announced in a July 15, 2022 news item on Nanowerk but first, there’s an explanation of why this server is needed,

Diseases of genetic cause can be investigated by inducing the respective mutations in cell lines that are then used to model human diseases. The overall aim is to elucidate underlying mechanisms, interactions with environmental factors and ideally to find curative strategies.

A crucial step in generating genetically modified cell models 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 support scientists with the comparison, different workflows and software are available, but many of them require expensive high-tier sequencers or manual curation efforts.

A July 15, 2022 IUF – Leibniz-Institut für umweltmedizinische Forschung (Leibniz Research Institute for Environmental Medicine) press release, which originated the news item, includes details about the server,

To address this issue, a team of scientists from the Genome Engineering and Model Development lab at the IUF – Leibniz Research Institute for Environmental Medicine in Düsseldorf, led by Dr. Andrea Rossi, developed a robust, versatile, and easy-to-use computational webserver named CRISPRnano (https://www.crisprnano.de/) that enables the analysis of noisy reads generated by affordable and portable sequencers including Oxford Nanopore Technologies (ONT) devices. CRISPRnano allows fast and accurate identification, quantification, and visualization of genetically modified cell lines, it is compatible with Next Generation Sequencing (NGS) and ONT sequencing reads, and it can be used without an internet connection. The according study was published in the renowned scientific journal Nucleic Acids Research.

Here’s a link to and a citation for the related study,

Identification of genome edited cells using CRISPRnano by Thach Nguyen, Haribaskar Ramachandran, Soraia Martins, Jean Krutmann, Andrea Rossi. Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W199–W203, DOI: https://doi.org/10.1093/nar/gkac440 Published: 30 May 2022

This paper appears to be open access.