Exome-based RetNet panel analysis in a Belgian cohort with inherited retinal disease expands the molecular and phenotypic spectrum of recently identified iRD genes

Abstract

Purpose : Inherited retinal diseases (iRD) are caused by mutations in over 260 disease genes and display a broad phenotypic spectrum, ranging from isolated to syndromic disease. We performed a comprehensive genetic analysis of the currently known disease genes (RetNet panel) in 220 iRD probands using whole exome sequencing (WES).

Methods : Enrichment was performed using the SureSelectXT Human All Exon V5/V6 kit (Agilent), followed by paired-end sequencing on a NextSeq 500 or HiSeq 3000 (Illumina). Read processing and variant calling was performed using the CLC Genomics Workbench (Qiagen). Alamut Batch was used for variant annotation of variants located in RetNet genes (https://sph.uth.edu/retnet). Identified mutations were confirmed using Sanger sequencing.

Results : Mutations were found in frequently mutated as well as in rare disease genes. Specifically, ARL3 was recently proposed as a novel disease gene for autosomal dominant retinitis pigmentosa (ADRP) following the identification of a missense variant c.269A>G (p.Tyr90Cys) in a single family. Interestingly, we identified the same ARL3 variant in a family segregating RP in three generations, and a novel missense variant in a simplex RP patient, corroborating the involvement of ARL3 in ADRP. Second, a patient with simplex RP was found to be homozygous for a novel frameshift variant in RAX2, in which only mono-allelic mutations have been described so far in cone-rod dystrophy and age-related macular dystrophy. Third, we identified a novel ARL2BP translational readthrough variant in a compound heterozygous state with p.Met45Arg in two unrelated probands with reported non-syndromic iRD. Finally, bi-allelic truncating variants in CEP164 and BBS2, expected to cause syndromic iRD, were found in two probands diagnosed with non-syndromic iRD, challenging the hypothesis that null mutations underlie the most severe end of the phenotypic spectrum.

Conclusions : Overall, RetNet-WES analysis revealed an underlying genetic defect in 55% of a Belgian iRD cohort. Apart from variants in more frequently mutated iRD genes, likely pathogenic variants were found in recently reported genes, supporting their role in iRD (ARL3), expanding their inheritance patterns (RAX2) and providing new insights into phenotypic consequences of bi-allelic loss-of-function alleles (ARL2BP, CEP164 and BBS2).

This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.