Gene analysis tool that overcomes challenges with CRISPR editing developed

Tokyo: In a significant discovery, a team of researchers has developed a software tool called DANGER (Deleterious and ANticipatable Guides Evaluated by RNA-sequencing) analysis that provides a way for the safer design of genome editing in all organisms.

For about a decade, researchers have used the CRISPR technology for genome editing. However, there are some challenges in the use of CRISPR.

The DANGER analysis overcomes these challenges and allows researchers to perform safer on and off-target assessments without a reference genome, said the study published in the journal Bioinformatics Advances.

The discovery holds the potential for applications in medicine, agriculture, and biological research.

“The design of genome editing requires a well-characterised genomic sequence. However, the genomic information of patients, cancers, and uncharacterised organisms is often incomplete,” said Kazuki Nakamae, an assistant professor at the Genome Editing Innovation Center, Hiroshima University.

CRISPR-Cas9 is a well-known gene editing technology. However, gene editing using CRISPR technology presents some challenges. The first challenge is that the phenotypic, or observable, effects caused by unexpected CRISPR dynamics are not quantitatively monitored.

The second challenge is that the CRISPR technology generally depends on basic genomic data, including the reference genome. The reference genome is like a template that provides researchers with general information on the genome.

Unexpected sequence editing with mismatches can occur, the authors wrote. The DANGER analysis software overcomes these challenges, they added.

The DANGER analysis quantified the phenotypic risk at the gene ontology term level, without a reference genome.

This success showed that DANGER analysis can be performed on various organisms, personal human genomes, and atypical genomes created by diseases and viruses. Looking ahead, the team hopes to expand their research using the DANGER analysis.

“We will apply the software to various genome editing samples from patients and crops to clarify the phenotypic effect and establish safer strategies for genome editing,” said Nakamae.