Novel Candidate Genes and a Wide Spectrum of Structural and Point Mutations Responsible for Inherited Retinal Dystrophies Revealed by Exome Sequencing

Abstract

BackgroundNGS-based genetic diagnosis has completely revolutionized the human genetics field. In this study, we have aimed to identify new genes and mutations by Whole Exome Sequencing (WES) responsible for inherited retinal dystrophies (IRD).MethodsA cohort of 33 pedigrees affected with a variety of retinal disorders was analysed by WES. Initial prioritization analysis included around 300 IRD-associated genes. In non-diagnosed families a search for pathogenic mutations in novel genes was undertaken.ResultsGenetic diagnosis was attained in 18 families. Moreover, a plausible candidate is proposed for 10 more cases. Two thirds of the mutations were novel, including 4 chromosomal rearrangements, which expand the IRD allelic heterogeneity and highlight the contribution of private mutations. Our results prompted clinical re-evaluation of some patients resulting in assignment to a syndromic instead of non-syndromic IRD. Notably, WES unveiled four new candidates for non-syndromic IRD: SEMA6B, CEP78, CEP250, SCLT1, the two latter previously associated to syndromic disorders. We provide functional data supporting that missense mutations in CEP250 alter cilia formation.ConclusionThe diagnostic efficiency of WES, and strictly following the ACMG/AMP criteria is 55% in reported causative genes or functionally supported new candidates, plus 30% families in which likely pathogenic or VGUS/VUS variants were identified in plausible candidates. Our results highlight the clinical utility of WES for molecular diagnosis of IRD, provide a wider spectrum of mutations and concomitant genetic variants, and challenge our view on syndromic vs non-syndromic, and causative vs modifier genes.

Functional characterization of the first missense variant in CEP78 , a founder allele associated with cone‐rod dystrophy, hearing loss, and reduced male fertility

“…Several studies have linked CEP78 ‐truncating variants with a unique CRDHL phenotype and, so far, all described variants are frameshift or splice site sequence variants with a presumed LOF effect. Recently, a homozygous structural variant affecting CEP78 , that is, a deletion‐inversion‐deletion, has also been described in a patient with CRDHL (Table S13; Fu et al, 2016; Namburi et al, 2016; Nikopoulos et al, 2016; Sanchis‐Juan et al, 2018; de Castro‐Miró et al, 2016). Here, we report the first missense variant causing CRDHL, c.449T>C, p.(Leu150Ser), expanding the CEP78 molecular spectrum.…”

“…Up to now, seven different truncating mutations have been reported in CEP78 , segregating in CRDHL families of different origins (Fu et al, 2016; Namburi et al, 2016; Nikopoulos et al, 2016). Furthermore, a homozygous CEP78 ‐truncating variant was found in a family with reported nonsyndromic RP (MIM# 268000; de Castro‐Miró et al, 2016). So far, only frameshift and splice site variants have been identified, with the latter all displaying exon skipping at the RNA level (Fu et al, 2016; Namburi et al, 2016; Nikopoulos et al, 2016).…”

Novel mutation in the choroideremia gene and multi-Mendelian phenotypes in Spanish families

“…Paired-end multiplex libraries, sequence enrichment, base read pairs, base calling, quality control and data processing were performed with the Illumina RTA sequence analysis pipeline as previously described 9. The results were mapped to the human genome assembly GRCh37.75 and annotated against Human dbSNP V. 137 IDs, population frequencies from the 1000 Genomes Project10 and Exome Variant Server,11 and several conservation and pathogenicity prediction algorithms from dbNSFP12 using snpSift 13…”

“…The PCR and sequencing primers are available on request. Pathogenicity scores for the variants identified were evaluated by several prediction algorithms (eg, MutationTaster, PolyPhen2, SIFT and NetGene2) as described elsewhere 9. Pathogenicity was also assessed by cosegregation analysis in the family.…”

Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India

“…Studies have shown that NGS of gene panels leads to higher detection of a genetic cause for retinal disease than traditional methods such as Sanger sequencing; however, these studies often have features that do not reflect clinical practice and may prevent extrapolation of reported diagnostic rates to clinical practice. Some studies recruited patients and often their families, while others heavily weighed in silico predictions for classifying missense variants as pathogenic and only one of these studies took into account American College of Medical Genetics and Genomics (ACMG) criteria for classifying variants, which puts low value on in silico predictions (Audo et al, ; Bernardis et al, ; Carss et al, ; de Castro‐Miro et al, ; Glockle et al, ; O'Sullivan et al, ; Riera et al, ). Some studies investigated only subsets of patients or patients with well‐defined phenotypes (Audo et al, ; Licastro et al, ; O'Sullivan et al, ).…”