Whole genome sequencing of CRISPR/Cas9-engineered NF-κB reporter mice for validation and variant discovery

Abstract Targeted knockout, mutations, or knock-in of genomic DNA fragments in model organisms have been used widely for functional and cell-tracking studies. The desired genetic perturbation is often accomplished by recombination-based or CRISPR/Cas9-based genome engineering. For validating the intended genetic modification, a local region surrounding the targeted locus is typically examined based on enzymatic cleavage and consequent length patterns, e.g. in a Southern analysis. Despite its wide use, this approach is open to incomplete and ambiguous readouts. With decreasing costs of high-throughput sequencing, it is becoming feasible to consider a large-scale validation of a new strain after a targeted genetic perturbation. Here we describe a dataset of whole-genome sequences and the variant analysis results from four novel reporter mouse strains. This served to validate the strains and identified all the off-target effects on the genome, thereby increasing the genetic diversity of genomic sequences over those represented in the public databases for inbred mice.