A team of researchers has developed a software tool that provides a way for the safer design of genome editing in all organisms with a transcriptome. For about a decade, researchers have used the CRISPR technology for genome editing. However, there are some challenges in the use of CRISPR.
The new analysis system overcomes these challenges and allows researchers to perform safer on- and off-target assessments without a reference genome. It holds the potential for applications in medicine, agriculture, and biological research.A team of researchers has developed a software tool called DANGER analysis that provides a way for the safer design of genome editing in all organisms with a transcriptome. For about a decade, researchers have used the CRISPR technology for genome editing.
A 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. These off-target sites are always unexpected. So researchers need a way to observe factual genomic sequences and limit potential off-target effects.
The team demonstrated that the DANGER analysis pipeline achieves several goals. It detected potential DNA on- and off-target sites in the mRNA-transcribed region on the genome using RNA-sequencing data. It evaluated phenotypic effects by deleterious off-target sites based on the evidence provided by gene expression changes. It quantified the phenotypic risk at the gene ontology term level, without a reference genome.
DANGER analysis is open-source and freely adjustable. So the algorithm of this pipeline could be repurposed for the analysis of various genome editing systems beyond the CRISPR-Cas9 system. It is also possible to enhance the specificity of DANGER analysis for CRISPR-Cas9 by incorporating CRISPR-Cas9-specific off-target scoring algorithms. The team believes that the DANGER analysis pipeline will expand the scope of genomic studies and industrial applications using genome editing.
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