Significance Antigen-specific immunotherapy may be improved by focusing on epitopes that are disease-relevant and known to be presented on an individual’s human leukocyte antigen (HLA) haplotype, while targeting T cells across multiple antigens and including specific neoepitopes that are not present in protein antigens and/or not produced beyond inflamed sites. Here, we provide proof of principle that such a strategy applied to tolerogenic DNA vaccination is effective in a preclinical model of autoimmune diabetes, paving the way for precision medicine using endogenously encoded epitopes. It takes a minimum number of regular treatments to achieve a level of tolerance and regulation that is needed to limit insulitis and provide sustained protection before treatment may be discontinued or reduced in frequency.