Fig. 2. In vivo assessment of the on-target site.

a Breakup of sequencing results of the on-target site in the genome-edited clones amplified from the retina collected 1 M or 3 M post-injection. MMEJ, NoMHA, and NoTS represents injection of protype MMEJ vector, MMEJ vector without microhomology arms, and MMEJ vector without gRNA target sites, respectively. HITI represents homology-independent targeted integration. See Supplementary Fig. 3 for vector map. Total clones sequenced were 57, 70, 67, 64 and 86 for MMEJ (1 M), MMEJ (3 M), NoMHA (1 M), NoTS (1 M), and HITI (1 M), respectively. Success indicates successful mutation replacement. Cleavage site indel represents indels in either gRNA cleavage site without replacement of IRD2 mutation (see Online Methods for detail). Note, co-existing mutation replacement and cleavage site indels, which is expected to occur as a consequence of repeated cleavage at the gRNA site was not observed. b Total editing rate. Percentage of clones that showed any sign of genome editing among the total clones analyzed. c Absolute success rate in the rods, assuming the cells comprise 75% of retinal neurons. d Estimation of detection efficiency of Success allele by subcloning and PCR. Observed % Success (vertical axis) were obtained by distinguishing the identity of the clones derived from PCR products amplified from mixture of Success and unedited mutant DNA templates at various ratio (horizontal axis). Total clones sequenced in this experiment were 61, 52, 64 and 61 for 5%, 10%, 20%, and 50% mixtures (rate of Success DNA versus total DNA), respectively. Intercept = −0.154, slope = 0.528, r² = 0.99. e Estimated absolute success rate in the rods corrected for by the detection efficiency of Success alleles relative to unedited mutant allele, assuming 75% of retinal neurons are the rods. f RT-PCR of Gnat1 at 1 M (N = 4) and 3 M (N = 3). g RT-PCR of SaCas9 at 1 M (N = 4) and 3 M (N = 3) post-injection. h. RT-PCR of gRNA at 1 M (N = 4), and 3 M (N = 3) post-injection. Data represent the mean ± S.E.M. Source data are provided as a Source Data file.