Figure 3.

PD-1-targeting CRISPR-Cas9 generates consistent on- and off-target genomic profiles

(A) Fraction of frameshift (white bars) and in-frame indels (black) as a percentage of total indels in edited samples throughout the REP. The median of 10 samples for each category is displayed, and each sample is represented by two replicates. (B) REP day 14 contribution of top three indels (−16 bp, black; +1 bp, dark gray; -1 bp, light gray) to total indels shown as percentage of total indels for each sample. Remaining indels are represented by “Other” (white). Each sample is represented by two replicates, and average expression is shown. (C) Base-pair-level depiction of PDCD1-targeting gRNA binding to a potential off-target site (black bars). Base-pair mismatches are faded out. Protospacer adjacent motif (PAM) for Cas9 binding is in boldface. Chromosomal location, strand direction, and sense are annotated. Created with BioRender.com. (D) Representative off-target IDAA assay plot from REP day 14 samples. Wild-type amplicon is shown in yellow.