This paper is being retracted because the genomic variants observed by the authors in two CRISPR-treated mice cannot be conclusively attributed to CRISPR–Cas9. The paper was a peer-reviewed Correspondence in the journal. The authors made their observation as part of their work on correction of a gene involved in blindness. The authors used mice of the inbred FVB/NJ strain from the JAX genetic quality control program that were purchased within months of each other and that were not bred in the authors' laboratory. The assumption was that this design was sufficient to control for genetic variation in an inbred strain. Since publication of the work, however, it has been brought to the journal's and the authors' attention that without parental controls or more analysis of genetic background, it is not certain that the variants reported are due to CRISPR treatment (https://doi.org/10.1038/nmeth.4559, https://doi.org/10.1038/nmeth.4552, https://doi.org/10.1038/nmeth.4553, https://doi.org/10.1038/nmeth.4541, https://doi.org/10.1038/nmeth.4554). The study is therefore being retracted to maintain the accuracy of the scientific record. S.H.T. and W.-H.W. agree with the retraction. K.A.S., D.F.C., A.G.B. and V.B.M. do not agree with the retraction. All authors note that there is very little whole-genome sequencing data on the effects of CRISPR treatment in vivo. The question of whether CRISPR has effects on the in vivo genome will require further study; the authors are carrying out follow-up studies using whole-genome sequencing.