In vivo CRISPR-Cas gene editing with no detectable genome-wide off-target mutations

CRISPR-Cas genome-editing nucleases hold substantial promise for human therapeutics but identifying unwanted off-target mutations remains an important requirement for clinical translation. For ex vivo therapeutic applications, previously published cell-based genome-wide methods provide potentially useful strategies to identify and quantify these off-target mutation sites. However, a well-validated method that can reliably identify off-targets in vivo has not been described to date, leaving the question of whether and how frequently these types of mutations occur. Here we describe Verification of In Vivo Off-targets (VIVO), a highly sensitive, unbiased, and generalizable strategy that we show can robustly identify genome-wide CRISPR-Cas nuclease off-target effects in vivo. To our knowledge, these studies provide the first demonstration that CRISPR-Cas nucleases can induce substantial off-target mutations in vivo, a result we obtained using a guide RNA (gRNA) deliberately designed to be promiscuous. More importantly, we used VIVO to show that more appropriately designed gRNAs can direct efficient in vivo editing with no detectable off-target mutations. VIVO provides a general strategy for defining and quantifying in vivo off-target effects of gene-editing nucleases in whole organisms, thereby providing a framework that should encourage further development of in vivo genome editing therapeutic strategies.