Fig. 5

Genetic variation in HEK293 induces allele-specific Cas9 cleavage. a An IGV image showing SMRT-OTS alignments (top) and HEK293 HiFi SMRT sequencing reads (bottom) in a window surrounding a predicted gRNA site for ATXN10 (chr9:109,570,956; GRCh38 coordinates). The HiFi reads reveal a heterozygous SNV (rs7861875; T>C) in HEK293 within the ATXN10 gRNA binding site, where the reference allele (T) is linked to the alternative alleles of several other heterozygous SNVs in the window. In the SMRT-OTS data, 101 of the 106 reads (95%) of the reads correspond to the haplotype having the alternative rs7861875 allele (G). b Schematic view of allele specific ATXN10 gRNA binding at the rs7861875 locus. The CRISPR-Cas9 complex does not bind to the rs7861875 reference allele (T), which has three mismatches to the gRNA sequence (bottom). It binds more efficiently to the alternative allele (c) which has only two mismatches to the ATXN10 gRNA sequence (top)