The implementation of Next Generation Sequencing (NGS) technology in the clinical laboratory has allowed for large-scale panel testing of many genes simultaneously at a reduced cost and turn-around time. Our laboratory has utilized NGS technology to develop large gene panels designed to target genes associated with specific clinical phenotypes, including autism spectrum disorders and eye-related disorders. Our results indicate that targeted panel based testing and a tiered approach is likely to result in a greater diagnostic yield for autism spectrum disorders and eye related disorders.