A Multi-Strategy Sequencing Workflow in Inherited Retinal Dystrophies: Routine Diagnosis, Addressing Unsolved Cases and Candidate Genes Identification

Abstract

This article belongs to the Special Issue Inherited Retinal Diseases. ; The management of unsolved inherited retinal dystrophies (IRD) cases is challenging since no standard pipelines have been established. This study aimed to define a diagnostic algorithm useful for the diagnostic routine and to address unsolved cases. Here, we applied a Next-Generation Sequencing-based workflow, including a first step of panel sequencing (PS) followed by clinical-exome sequencing (CES) and whole-exome sequencing (WES), in 46 IRD patients belonging to 42 families. Twenty-six likely causal variants in retinal genes were found by PS and CES. CES and WES allowed proposing two novel candidate loci (WDFY3 and a X-linked region including CITED1), both abundantly expressed in human retina according to RT-PCR and immunohistochemistry. After comparison studies, PS showed the best quality and cost values, CES and WES involved similar analytical efforts and WES presented the highest diagnostic yield. These results reinforce the relevance of panels as a first step in the diagnostic routine and suggest WES as the next strategy for unsolved cases, reserving CES for the simultaneous study of multiple conditions. Standardizing this algorithm would enhance the efficiency and equity of clinical genetics practice. Furthermore, the identified candidate genes could contribute to increase the diagnostic yield and expand the mutational spectrum in these disorders. ; This work was supported by the Instituto de Salud Carlos III (ISCIII), Spanish Ministry of Economy and Competitiveness, Spain and co-funded by European Union (ERDF, "A way to make Europe") (PI15-01648 and PI18-00612, to G.A.), Regional Ministry of Health and Families of the Autonomous Government of Andalusia (PEER-0501-2019, to G.A.) and the Foundation Isabel Gemio/Foundation Cajasol (FGEMIO-2019-01, to G.A.). The CIBERER is an initiative of the ISCIII, Spanish Ministry of Economy and Competitiveness. EFS is supported by fellowship FI19/00091 from ISCIII and co-funded by ESF, "Investing in your future". MMS is supported by a fellowship associated with the CTS-1664 project, which has been funded by the Regional Ministry of Economy, Knowledge, Enterprise, and University of the Regional Government of Andalusia.