Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome.

Christine Neuhaus,Hesham M Taha,Dagmar Huhle,Diana Mitter,Susanne Markus,Raoul Heller,Heidi Stöhr,Hanno J Bolz,Kerstin Nagel-Wolfrum,Ute Steinhauer,Tobias Eisenberger,Christian Decker,Arif O Khan,Fabian Moeller,Klaus Rüther,Markus Pfister,Cornelie Müller-Hofstede,Sandra Nagl,Klaus Rohrschneider,Peter Charbel Issa,Solaf M Elsayed,Birgit Lorenz,Ingo Kennerknecht,Markus N Preising ,Bodo B Beck ,Heike Korbmacher ,C A Blank ,Shahid Mahmood Baig

doi:10.1002/mgg3.312

Abstract

BackgroundCombined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP).MethodsSanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array‐CGH were conducted in 138 patients clinically diagnosed with Usher syndrome.ResultsA molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively. Quantitative readout reliably detected CNVs (confirmed by MLPA or array‐CGH), qualifying targeted NGS as one tool for detecting point mutations and CNVs. CNVs accounted for 10% of identified USH2A alleles, often in trans to seemingly monoallelic point mutations. We demonstrate PTC124‐induced read‐through of the common p.Trp3955* nonsense mutation (13% of detected USH2A alleles), a potential therapy target. Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3, genes implicated in isolated deafness and RP. Two patients with additional enamel dysplasia had biallelic PEX26 mutations, for the first time linking this gene to Heimler syndrome.ConclusionTargeted NGS not restricted to Usher genes proved beneficial in uncovering conditions mimicking Usher syndrome.

Highlights

The co-occurrence of bilateral hearing impairment and visual impairment, if due to retinal degeneration, is of genetic origin in most cases in industrial countries
A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively
Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3, genes implicated in isolated deafness and retinitis pigmentosa (RP)

Summary

Introduction

The co-occurrence of bilateral hearing impairment (here comprehensively termed “deafness”) and visual impairment, if due to retinal degeneration, is of genetic origin in most cases in industrial countries. The by far most prevalent causes are mutations in the 11 genes (MYO7A, OMIM *276903; USH1C, OMIM *605242; CDH23, OMIM *605516; PCDH15, OMIM *605514; USH1G, OMIM *607696; CIB2, OMIM *605564; USH2A, OMIM *608400; ADGRV1, OMIM *602851; DFNB31/WHRN, OMIM *607928; CLRN1, OMIM *606397; PDZD7, OMIM *612971) associated with Usher syndrome (Besnard et al 2014), an autosomal recessive trait characterized by congenital deafness and RP in the first decade (in type 1, USH1; about 35% of cases (Petit 2001)) or by progressive hearing loss and RP of later onset in USH2 (about two thirds of patients). Simultaneous homozygosity for mutations in genes associated with isolated retinal degeneration and hearing loss (OTOA, OMIM *607038 and NR2E3, OMIM *604485), and mutations in PEX26 (OMIM *608666) in patients with additional enamel dysplasia demonstrate how rare, genetically distinct entities may mimic Usher syndrome. Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP)

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Conclusion