Chimeric antigen receptor (CAR) T cell immunotherapies have been transformative solutions to treat both adult and pediatric patients with a variety of cancers. Given that CAR T cell therapies involve genetic alterations of a patient’s T cells by introduction of the CAR into host cells using lentiviral vectors, the quality of CAR T cell therapies are extensively regulated to warrant efficacy and safety. Key safety and efficacy attributes need to be accurately measured prior to reintroducing modified T cells back into patients, including CAR transgene copy number or viral vector copy number (VCN). 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. Mission Bio has developed an end-to-end solution from panel design to data analysis for single-cell targeted DNA sequencing to interrogate transgenes. 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.