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Summary: Duchenne muscular dystrophy (DMD) is a severe muscle-degenerative disease caused by a mutation in the dystrophin gene. Genetic correction of patient-derived induced pluripotent stem cells (iPSCs) by TALENs or CRISPR-Cas9 holds promise for DMD gene therapy; however, the safety of such nuclease treatment must be determined. Using a unique k-mer database, we systematically identified a unique target region that reduces off-target sites. To restore the dystrophin protein, we performed three correction methods (exon skipping, frameshifting, and exon knockin) in DMD-patient-derived iPSCs, and found that exon knockin was the most effective approach. We further investigated the genomic integrity by karyotyping, copy number variation array, and exome sequencing to identify clones with a minimal mutation load. Finally, we differentiated the corrected iPSCs toward skeletal muscle cells and successfully detected the expression of full-length dystrophin protein. These results provide an important framework for developing iPSC-based gene therapy for genetic disorders using programmable nucleases. : Using the TALEN and CRISPR-Cas9 systems, Hotta and colleagues restored the disease-causing mutation of the dystrophin gene by exon skipping, frameshift, and exon knockin approaches in Duchenne muscular dystrophy patient-derived iPSCs. Rigorous genomic integrity tests identified no severe off-target mutagenesis in the corrected iPSC clones, suggesting that both systems are promising tools for personalized gene therapy using iPSCs.