Abstract
Purpose :
Inherited retinal degenerations (IRDs) are the primary cause of working age blind registration in Western countries. These rare disease are genetically heterogeneous (>300 known genetic loci) and genetic diagnosis is required for many novel therapies (e.g., gene therapy). First-tier genetic testing of IRDs with panel-based next generation sequencing (pNGS) has a diagnostic yield of ~70-80% leaving the remaining more challenging cases to be resolved by second-tier testing methods.
Methods :
Patients on a large hospital-based IRD register in Ireland were clinically and genetically assessed. 84% of this cohort was genetically resolved from 1st tier pNGS (250 genes). Non-resolved cases (n=69) were clinically reassessed with 26% (n=18) being reclassified as non-IRD disease. 34 patients were available for further genetic testing, all providing informed consent. Autosomal recessive cases with 1 candidate variant underwent single gene testing (introns and exons). Cases with inadequate pNGS coverage had repeat pNGS (250 genes) while those with adequate initial panel coverage had an expanded panel (351 genes) or trio whole exome sequencing (WES).
Results :
Removing non-IRD cases from consideration and utilizing case-appropriate 2nd-tier genetic testing techniques, we genetically resolved 56% of previously unresolved pedigrees bringing the overall resolve rate to 92% (388/423). Resolution rate by test was pNGS 100% (n=5), single gene test 44% (n=4/9), trio WES 25% (1/4). 4 novel variants were found, 1 each in ABCA4, EYS, FLVCR1, and RPGR . 15.6% of the cohort resolved by 2nd line testing approaches are eligible for current gene therapy clinical trials (RPGR).
Conclusions :
Though novel techniques like WGS will supersede current techniques, at present pNGS remains the most cost effective first-tier approach for molecular assessment of diverse IRD populations (€600 for NGS vs mean €1,222 for all other test types per positive result). Second-tier genetic testing should be guided by clinical (i.e., reassessment, multimodal imaging, electrophysiology) and genetic (i.e. single alleles in autosomal recessive disease) indications to achieve a genetic diagnosis in the most cost-effective manner. See Figure 1.
This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.