A reanalysis of Schaefer et al. does not indicate extensive CRISPR/Cas9 mediated off-target editing events

Recently Schaefer et al. (1) reported the presence of more than a thousand genomic differences between mice that had been edited with S. pyogenes Cas9 at the zygote stage, and a control mouse of the same strain. Given the overlap of genomic differences between the two edited mice that were not found in the control mouse, the authors concluded that these differences arose from a Cas9-dependent activity. We feel that this conclusion is inappropriate, for three key reasons: 1) there was incomplete analysis of the genetic variation; 2) there was no consideration that the variation is naturally arising in these animals; and 3) the inferred behavior of Cas9 lies outside of its understood mechanism of action. Attribution to Cas9 activity should require a burden of proof, that we believe has not been met.