Human genetic diversity alters therapeutic gene editing off-target outcomes

CRISPR gene editing holds great promise to modify somatic genomes to ameliorate disease. In silico prediction of homologous sites coupled with biochemical evaluation of possible genomic off-targets may predict genotoxicity risk of individual gene editing reagents. However, standard computational and biochemical methods focus on reference genomes and do not consider the impact of genetic diversity on off-target potential. Here we developed a web application called CRISPRme that explicitly integrates human genetic variant to nominate and prioritize off-target sites at scale. The method considers both single-nucleotide variants (SNVs) and indels, accounts for bona fide haplotypes and is suitable for personal genome analyses. We tested CRISPRme with a gRNA targeting the BCL11A erythroid enhancer that has shown therapeutic promise in clinical trials for sickle cell disease (SCD) and β-thalassemia. We find that the top candidate off-target is produced by a non-reference allele common in African-ancestry populations. We validate that SpCas9 generates indels and chr2 pericentric inversions in a strictly allele-specific manner in edited hematopoietic stem/progenitor cells. CRISPRme highlights alternative allele-specific off-target editing as a prevalent risk of gRNAs considered for therapeutic gene editing. Our report illustrates how population and private genetic variants should be considered as modifiers of genome editing outcomes.