biostudies-literatureCancellieri SDoris Duke Charitable FoundationBurroughs Wellcome FundNHLBI NIH HHSSt. Jude Children’s Research HospitalNHGRI NIH HHSU.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood InstituteU.S. Department of Health & Human Services | NIH | National Human Genome Research Institute34-43https://www.ebi.ac.uk/biostudies/studies/S-EPMC10272994biostudies-literatureUnknown55(1)CRISPR gene editing holds great promise to modify DNA sequences in somatic cells to treat disease. However, standard computational and biochemical methods to predict off-target potential focus on reference genomes. We developed an efficient tool called CRISPRme that considers single-nucleotide polymorphism (SNP) and indel genetic variants to nominate and prioritize off-target sites. We tested the software with a BCL11A enhancer targeting guide RNA (gRNA) showing promise in clinical trials for sickle cell disease and β-thalassemia and found that the top candidate off-target is produced by an allele common in African-ancestry populations (MAF 4.5%) that introduces a protospacer adjacent motif (PAM) sequence. We validated that SpCas9 generates strictly allele-specific indels and pericentric iNature geneticsHuman genetic diversity alters off-target outcomes of therapeutic gene editing.PMC10272994R35 HG010717P01HL053749P01 HL053749OT2 HL154984RM1 HG009490R35HG010717RM1HG009490OT2HL154984Giugno RPinello LArmant MNguyen MAWolfe SABauer DEBombieri NCancellieri SKatta VTognon MLin LYZeng JTsai SQLin JCiuculescu MFMaitland SAfalseHuman genetic diversity alters off-target outcomes of therapeutic gene editing.CRISPR gene editing holds great promise to modify DNA sequences in somatic cells to treat disease. However, standard computational and biochemical methods to predict off-target potential focus on reference genomes. We developed an efficient tool called CRISPRme that considers single-nucleotide polymorphism (SNP) and indel genetic variants to nominate and prioritize off-target sites. We tested the software with a BCL11A enhancer targeting guide RNA (gRNA) showing promise in clinical trials for sickle cell disease and β-thalassemia and found that the top candidate off-target is produced by an allele common in African-ancestry populations (MAF 4.5%) that introduces a protospacer adjacent motif (PAM) sequence. We validated that SpCas9 generates strictly allele-specific indels and pericentric i2023-01-01T00:00:00Z2023 Jan2026-04-29T02:37:59.798Z2024-11-09T00:25:01.848ZS-EPMC102729943652243210.1038/s41588-022-01257-y