Panel-based NGS Reveals Novel Pathogenic Mutations in Autosomal Recessive Retinitis Pigmentosa.

Raquel Perez-Carro,Rosa Riveiro-Alvarez,Almudena Avila-Fernandez,Noelia Sanchez-Bolivar,Rocío Sánchez-Alcudia,Christian Gilissen,Mª Isabel López-Molina,Olga Zurita,Carmen Ayuso,Marta Corton,Fiona Blanco-Kelly,Miguel Angel Lopez-Martinez,Stefan H Lelieveld,Iker Sánchez-Navarro,Patricia Fernandez-San Jose,Jose M Millan,Elena Aller

doi:10.1038/srep19531

Abstract

Retinitis pigmentosa (RP) is a group of inherited progressive retinal dystrophies (RD) characterized by photoreceptor degeneration. RP is highly heterogeneous both clinically and genetically, which complicates the identification of causative genes and mutations. Targeted next-generation sequencing (NGS) has been demonstrated to be an effective strategy for the detection of mutations in RP. In our study, an in-house gene panel comprising 75 known RP genes was used to analyze a cohort of 47 unrelated Spanish families pre-classified as autosomal recessive or isolated RP. Disease-causing mutations were found in 27 out of 47 cases achieving a mutation detection rate of 57.4%. In total, 33 pathogenic mutations were identified, 20 of which were novel mutations (60.6%). Furthermore, not only single nucleotide variations but also copy-number variations, including three large deletions in the USH2A and EYS genes, were identified. Finally seven out of 27 families, displaying mutations in the ABCA4, RP1, RP2 and USH2A genes, could be genetically or clinically reclassified. These results demonstrate the potential of our panel-based NGS strategy in RP diagnosis.

Highlights

Hitherto, nearly 3100 pathogenic mutations have been reported[8,9] in more than 80 genes associated with non-syndromic Retinitis pigmentosa (RP) and 55 of them have been related to autosomal recessive RP (RetNet; update Aug 2015 https://sph.uth.edu/retnet/)
Genetic diagnosis of the retinal dystrophies (RD) has been mainly based on either the use of the specific genotyping microarrays—for which the mutation detection rate ranges from 11% to 70% depending on the RD form10–12—or on a gene-by-gene analysis by Sanger sequencing for mutation screening which is time-consuming and expensive
The molecular diagnosis of patients affected with RD provides them a number of benefits as it can supply an accurate prognosis of the clinical course of the disease and appropriate genetic counseling to the families

Summary

Introduction

Nearly 3100 pathogenic mutations have been reported[8,9] in more than 80 genes associated with non-syndromic RP and 55 of them have been related to autosomal recessive RP (arRP) (RetNet; update Aug 2015 https://sph.uth.edu/retnet/). The molecular diagnosis of patients affected with RD provides them a number of benefits as it can supply an accurate prognosis of the clinical course of the disease and appropriate genetic counseling to the families. The molecular characterization of patients allows future inclusion in clinical trials based on gene therapy. In the last few years, the development of high-throughput technologies, such as next-generation sequencing (NGS), has allowed to screen a large number of genes. This technique offers a high sensitivity and efficiency making the molecular diagnosis of this heterogeneous disease easier. Recent studies in different populations demonstrated the great potential of NGS technologies as a diagnostic tool in the field of RD characterizing around 30-60% of cases[9,13]

Methods

Results

Conclusion