Retinal Targeted-Capture Next Generation Sequencing and CLIA Confirmation in a Representative Range of Patients with Inherited Retinal Degeneration

Abstract

Purpose: To determine the genetic cause of disease in a panel of clinically characterized retinal degeneration patients from Texas and surrounding states. This collection of genotype known, clinically-characterized patients will be a valuable resource for future clinical trials.

Methods: Patients with inherited retinal degeneration underwent complete ophthalmic exams and genetic consultations. Genomic DNA from each proband was analyzed for the presence of mutation in 163 retinal disease genes using a targeted-capture next-generation sequencing (NGS) research protocol. Di-deoxy sequencing validation of potential disease-causing variants was performed using CLIA protocols

Results: Forty-eight unrelated patients with a variety of retinal degenerations were tested. Twenty five (52%) had a diagnosis of retinitis pigmentosa (RP), ten (21%) had Leber’s congenital amaurosis, five (10%) had a form of cone dystrophy, three (6%) had Usher’s syndrome, and five (10%) had other rare forms of retinal degeneration. The majority of samples, 73%, were isolate in nature with no reported family history of retinal disease. Retinal targeted-capture NGS identified potentially pathogenic mutation(s) in 33 of the 48 patients tested. Pathogenicity analyses, including variant assessment and di-deoxy sequencing of probands and available family members, confirmed pathogenic or likely pathogenic mutations in 28 patients. Two additional patients were found to have variants of unknown significance in retinal disease associated genes. Pathogenic mutations were spread among 18 different genes.

Conclusions: Likely disease-causing mutations were identified in 58% of retinal degeneration patients. These genotype known patients are now an accessible, well characterized resource for enrollment in gene therapy and other clinical trials. This cohort of 48 patients is a pilot for “The Texas1000”, a project in development that aims to determine the genetic cause of retinal degeneration in 1,000 clinically characterized patients in Texas and nearby states.