A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies

Inherited retinal diseases (IRD) are a heterogeneous group of diseases that mainly affect the retina; more than 250 genes have been linked to the disease and more than 20 different clinical phenotypes have been described. This heterogeneity both at the clinical and genetic levels complicates the identification of causative mutations. Therefore, a detailed genetic characterization is important for genetic counselling and decisions regarding treatment. In this study, we developed a method consisting on pooled targeted next generation sequencing (NGS) that we applied to 316 eye disease related genes, followed by High Resolution Melting and copy number variation analysis. DNA from 115 unrelated test samples was pooled and samples with known mutations were used as positive controls to assess the sensitivity of our approach. Causal mutations for IRDs were found in 36 patients achieving a detection rate of 31.3%. Overall, 49 likely causative mutations were identified in characterized patients, 14 of which were first described in this study (28.6%). Our study shows that this new approach is a cost-effective tool for detection of causative mutations in patients with inherited retinopathies.This work was supported by grants from the National Institute of Health Carlos III (Institute of Health Carlos III/ISCIII) (CP10/00572, PI13/02621 and RD16/0008/0027 to JRE, PI17/01413 to CI, and a Research Intensification Contract to ALdM); the Basque Government's Industry Department (SAIOTEK: SAIO11-PE11BN002; and SAIO12-PC12BN001 to JRE), a grant from the Mutua Madrilena Foundation and support from the Retinitis Pigmentosa Patients of Gipuzkoa Foundation (BEGISARE). JR-E is a Miguel Servet II Fellow, National Institute of Health Carlos III (ISCIII). MEI was supported by grants from the Basque Government's Department of Education (DEDUC14/309). OB is supported by funding from the Retinitis Pigmentosa Patients of Gipuzkoa Foundation (BEGISARE) and a grant from the Mutua Madrilena Foundation. AA was supported by grants from the Fundacion Jesus de Gangoiti Barrera and from the Basque Government's Departments of Industry and Education (SAIOTEK-11BN002/PC12BN001/DEPLC13/002). CI is partially supported by a Research Intensification Contract (INTBIO15/001). The authors are grateful to Xabier Elcoroaristizabal and Marta Fernandez-Mercado for their helpful advice on developing the base-calling setup. Maribel Gomez; Naiara Telletxea and Nahikari Pastoriza at the Basque Biobank for isolating DNA samples; and Dr. Carmen Ayuso for kindly providing control samples. We also give special thanks to all patients with IRD and their families involved in the study