Cell and gene therapies are transformative solutions for a host of inherited and acquired diseases for which 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 therapeutic agents and is a key attribute for assessing their safety and efficacy. Yet, conventional methods for measuring gene transfer lack the resolution and representation to truly reflect sample composition and either report a population average (bulk) or involve laborious and time-consuming clonal outgrowth which can take weeks. Mission Bio has developed an end-to-end solution from panel design to data analysis for single-cell targeted DNA sequencing. Here, using the Tapestri platform we demonstrate that single-cell DNA sequencing identifies transduced versus non-transduced cells with exceptional accuracy and precision, as well as measures the single-cell level vector copy number (VCN) for populations of thousands of cells with single nucleotide resolution while reducing sample processing time from weeks to days.