Cell and gene therapies are transformative solutions for diseases where existing interventions are ineffective. Many such therapies rely on the introduction of transgenes into host cells using viral or non-viral vectors. The accurate measurement of gene transfer is critical to the development of such therapies and is critical for assessing their safety and efficacy. Yet, conventional methods for measuring gene transfer either report a population average (bulk) or involve laborious and time-consuming clonal outgrowth which can take up to 14 days. Mission Bio has developed an end-to-end solution from panel design to data analysis for single-cell targeted DNA sequencing. Using the Tapestri platform we demonstrate that single-cell DNA sequencing identifies transduced versus non-transduced cells with exceptional accuracy and precision for populations of up to 10,000 cells while reducing sample processing time from weeks to days.