An innovative strategy for the molecular diagnosis of Usher syndrome identifies causal biallelic mutations in 93% of European patients

Abstract

Usher syndrome (USH), the most prevalent cause of hereditary deafness–blindness, is an autosomal recessive and genetically heterogeneous disorder. Three clinical subtypes (USH1–3) are distinguishable based on the severity of the sensorineural hearing impairment, the presence or absence of vestibular dysfunction, and the age of onset of the retinitis pigmentosa. A total of 10 causal genes, 6 for USH1, 3 for USH2, and 1 for USH3, and an USH2 modifier gene, have been identified. A robust molecular diagnosis is required not only to improve genetic counseling, but also to advance gene therapy in USH patients. Here, we present an improved diagnostic strategy that is both cost- and time-effective. It relies on the sequential use of three different techniques to analyze selected genomic regions: targeted exome sequencing, comparative genome hybridization, and quantitative exon amplification. We screened a large cohort of 427 patients (139 USH1, 282 USH2, and six of undefined clinical subtype) from various European medical centers for mutations in all USH genes and the modifier gene. We identified a total of 421 different sequence variants predicted to be pathogenic, about half of which had not been previously reported. Remarkably, we detected large genomic rearrangements, most of which were novel and unique, in 9% of the patients. Thus, our strategy led to the identification of biallelic and monoallelic mutations in 92.7% and 5.8% of the USH patients, respectively. With an overall 98.5% mutation characterization rate, the diagnosis efficiency was substantially improved compared with previously reported methods.

Comprehensive Molecular Screening in Chinese Usher Syndrome Patients

“…Combined TES and Sanger-DNA direct sequencing determined that our overall mutation detection rate for the current cohort was 78.2%. This solving proportion is compatible with the reported rates in several previous studies using TES or Sanger-DNA direct sequencing 6,10,11,[26][27][28] ; however, it is still about 15% lower than the 92.7% rate reported recently by Bonnet et al 12 The mutation detection rate is related to the accuracy of the patients' clinical diagnoses. In our study, the mutation detection rate (85%) for USH1 patients was higher than that (76.8%) for USH2 patients.…”

“…28,31,33,34 In contrast, the most frequent USH2A mutations (p.Glu767Serfs*21, p.C3267R, and p.T3571M) in European patients were not detected in the current study. 6,12,40 For MYO7A, no frequent mutation was observed in the current cohort, which might be related with the small number of patients with MYO7A mutations.…”

“…12 Targeted NGS can detect a large genomic DNA arrangement; however, its capability to detect CNVs is related to the coverage depth. A recent study involving a Spanish cohort reported that the percentage of CNVs was 11.8%, and the researchers observed that the CNV analysis produced uncertain results in the target regions, with a coverage of less than 250x.…”

“…1 Recently, mutations of ABHD12, CEP250, and HARS have been described as causing atypical USH. 12 Additionally, PDZD7 has been proposed as a modifier gene for patients with mutations of USH2A and a contributor of digenic inheritance with GPR98. 13 What makes it more complicated is that mutations of USH2A may lead to RP without hearing loss, 14 and mutations of all six USH1 genes may cause non-syndrome deafness.…”

“…[6][7][8] Mutations of USH2A, GPR98, and DFNB31 are responsible for USH2 patients, and USH2A bears the main responsibility for this subtype (more than 60% of USH2 patients). 6,[9][10][11][12] The only USH3 gene is CLRN1. 1 Recently, mutations of ABHD12, CEP250, and HARS have been described as causing atypical USH.…”