Gene editing-based cell and gene therapy strategies often involve the delivery of a foreign DNA to the cell product or directly to the patient. For the efficacy and safety of such therapy strategies, we need to determine this DNA’s 1) on-target integration in the host 2) potential off-target integrations across the entire host genome 3) copy number of the integrated insert at each detected locus. Current NGS-based methods, relying on the sequencing of PCR enriched target DNA, fail to capture all types of integrations and cannot detect concatemerized integrations. Bionano Genomics Optical DNA mapping technology overcomes these barriers, by mapping long intact DNA molecules and by evaluating the entire genomic DNA directly without any PCR enrichment. We report its application in detecting a reporter cassette integration in embryonic stem cell lines and determination of the copy number of the integrated inserts.