Scheme of safety evaluation by DANGER analysis (IMAGE)

Hiroshima University

Scheme of safety evaluation by DANGER analysis

Caption

When off-target regions are affected by genome editing, unexpected changes in the mRNA quantity and sequence can emerge. The DANGER analysis is designed to analyze the effects from RNA-seq data at the Gene Ontology (GO) level. The DANGER analysis workflow includes:

  1. Initially, RNA-seq data from unedited samples is used to build a de novo transcriptome assembly, thereby identifying expressed sequences in the unedited samples.
  2. Based on the de novo transcriptome assembly and the expression profiles obtained in step 1, genomic regions with reduced expression in the edited sample's RNA-seq data are identified.
  3. The genomic regions where off-target effects are estimated from the expressed sequences, based on the de novo transcriptome assembly, are identified as potential off-target regions.
  4. The genomic regions detected in both steps 2 and 3 are inferred to be deleterious off-target regions.
  5. Gene ontology (GO) information on the deleterious off-target regions is retrieved from the public database.
  6. Considering both the number of deleterious off-target regions in each gene ontology and the sequence-specific features of these regions, their impact is quantified using an indicator called the Significant D-index, which estimates the risk to the phenotype.

Credit

Kazuki Nakamae and Hidemasa Bono, Hiroshima University

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