Next-Generation Sequencing Panel Results for Inherited Retinal Dystrophy in a Large Pediatric Cohort

Abstract

Purpose : Inherited retinal dystrophies (IRDs) are a genetically heterogenous group of disorders for which an early diagnosis may be essential. Approved therapies and clinical trials for many IRDs are most often contingent on a molecular diagnosis. Here, we report our experience with a comprehensive genetic testing strategy for inherited retinal dystrophy using a next-generation sequencing panel in a pediatric population.

Methods : We carried out a retrospective analysis of test results from 1,612 deidentified patients, aged 0 to 12 years, tested consecutively for IRDs using a retinal dystrophy panel at Blueprint Genetics. The molecular diagnoses of IRDs were based on the detection of variants that included mitochondrial variants, copy number variants (CNVs) including small CNVs defined by exon size, and non-coding variants in intron regions +/-20 bps from exon-intron boundaries. Variant interpretation was performed according to American College of Medical Genetics guidelines.

Results : We extracted information from the internal laboratory database. The median coverage of all target regions was 99.9% at >20X while the median sequencing depth was 208X. The median age at testing was 8 years. Males made up 59.7% (962) of the cohort while females made up 39.9%% (643). Sex was not specified for 7 (0.4%) patients. A molecular diagnosis was made in 906 (56.2%) patients while a variant of unknown significance (VUS) favoring pathogenic was identified in an additional 96 (6.0%). Diagnoses were made involving 114 genes; ABCA4, RS1, CNGB3, RPGR, and CEP290 accounted for 37.3% of diagnoses. Mitochondrial variants were responsible for 3 diagnoses. Copy number variants (CNV) contributed to the diagnosis in 71 patients (4.4%); 28/71 (39.4%) patients had CNVs that were 1 or 2 exons in size. Non-coding variants contributed to 171 (10.6%) diagnoses, 45/171 (26.3%) of which were beyond 10 base pairs from the exon-intron boundary.

Conclusions : These results support the clinical utility of genetic testing for IRDs in pediatric patients. Importantly, approved therapies or clinical trials are available for the 5 most common diagnostic genes. Small CNVs, noncoding variants beyond 10 base pairs from the exon-intron boundary, and mitochondrial variants were responsible for the diagnosis in 4.7% of patients, highlighting the importance of a comprehensive testing approach with high sensitivity to detect these variants.

This abstract was presented at the 2022 ARVO Annual Meeting, held in Denver, CO, May 1-4, 2022, and virtually.