The disclosure relates to methods of identifying a compound that comprises an epitope that induces immune tolerance in a patient suffering from an autoimmune disease. The disclosure further relates to methods of treating an autoimmune disease by administering (i) a compound identified by the methods described herein, (ii) regulatory T-cells from the patient or a compatible donor, or (iii) a combination of regulatory T-cells and a compound identified by the methods described herein. The disclosure further relates to methods of treating age- related macular degeneration and uveitis. The disclosure also relates to methods of monitoring, diagnosing and/or prognosticating an autoimmune disease in a patient.