• Usher syndrome
• biomarkers
• droplet digital PCR
• exon sequencing
• miRNA
• microarray

• Humans
• Usher Syndromes/genetics
• MicroRNAs/genetics
• Gene Expression Profiling/methods
• Myosin VIIa/genetics
• Cell Line
• Genotype
• Male
• Female
• Membrane Proteins/genetics
• Adult
• Cadherin Related Proteins
• Extracellular Matrix Proteins

• No Grant number available RYAN FOUNDATION

Usher Syndrome (USH) is the most common deaf-blind syndrome, affecting approximately 1 in 6000 people in the deaf population. This genetic condition is characterized by a combination of hearing loss (HL), retinitis pigmentosa, and, in some cases, vestibular areflexia. Among the subtypes of USH, USH type 1 is considered the most severe form, presenting profound bilateral congenital deafness, vestibular areflexia, and early onset RP. USH type 2 is the most common form, exhibiting congenital moderate to severe HL for low frequencies and severe to profound HL for high frequencies. Conversely, type 3 is the rarest, initially manifesting mild symptoms during childhood that become more prominent in the first decades of life. The dual impact of USH on both visual and auditory senses significantly impairs patients’ quality of life, restricting their daily activities and interactions with society. To date, 9 genes have been confirmed so far for USH: MYO7A, USH1C, CDH23, PCDH15, USH1G, USH2A, ADGRV1, WHRN and CLRN1. These genes are inherited in an autosomal recessive manner and encode proteins expressed in the inner ear and retina, leading to functional loss. Although non-genetic methods can assist in patient triage and disease extension evaluation, genetic and molecular tests play a pivotal role in providing genetic counseling, enabling appropriate gene therapy, and facilitating timely cochlear implantation (CI). The CRISPR/Cas9 system and viral-based gene replacement therapy have recently emerged as highly promising techniques for treating USH. Regarding drug therapy, PTC-124 and Nb54 have been identified as promising drug interventions for genetic HL in USH. Simultaneously, CI has proven to be critical in the restoration of hearing. This review aims to summarize the genetic and molecular diagnosis of USH and highlight the importance of early diagnosis in guiding appropriate treatment strategies and improving patient prognosis.

• Usher syndromes
• Hearing loss
• Retinitis pigmentosa
• Diagnosis
• Genetic therapies
• Cochlear implantation
• Quality of life

• deafblindness
• inherited retinal dystrophy
• inner ear
• pathogenic variant
• photoreceptor
• retinitis pigmentosa
• sensorineural hearing loss
• variant curation

• Animals
• Cadherin Related Proteins
• Cadherins/genetics
• Cell Cycle Proteins/genetics
• Ciliopathies/etiology
• Ciliopathies/pathology
• Cytoskeletal Proteins/genetics
• Disease Models, Animal
• Genetic Association Studies
• Humans
• Membrane Proteins/genetics
• Mutation
• Myosin VIIa/genetics
• Protein Interaction Maps/genetics
• Usher Syndromes/genetics
• Usher Syndromes/pathology

• PI19/00303 Instituto de Salud Carlos III
• PROMETEU/2018/135 Generalitat Valenciana

• Molecular diagnosis
• Syndromic hearing loss
• Targeted re-sequencing
• Usher syndrome

• Adolescent
• Adult
• Child
• Child, Preschool
• Chromosome Deletion
• Female
• Genetic Association Studies
• Genetic Predisposition to Disease
• Hearing/genetics
• Hearing Loss/diagnosis
• Hearing Loss/genetics
• Hearing Loss/physiopathology
• High-Throughput Nucleotide Sequencing
• Humans
• Infant
• Italy
• Male
• Middle Aged
• Mutation
• Phenotype
• Polymorphism, Single Nucleotide
• Predictive Value of Tests
• Syndrome
• Young Adult

• Animals
• Cadherins/metabolism
• Cell Adhesion/physiology
• Hair Cells, Auditory, Inner/physiology
• Hearing/physiology
• Mechanotransduction, Cellular
• Postural Balance/physiology

• R00 DC012534 NIDCD NIH HHS
• R01 DC015271 NIDCD NIH HHS

• MYO7A
• Mutation
• Targeted next generation sequencing
• Usher syndrome

Usher syndrome (USH) is the most common disease causing combined deafness and blindness. It is predominantly an autosomal recessive genetic disorder with occasionally digenic cases. Molecular diagnosis of USH patients is important for disease management. Few studies have tried to find the genetic cause of USH in Chinese patients. This study was designed to determine the mutation spectrum of Chinese USH patients.

We applied next generation sequencing to characterize the mutation spectrum in 67 independent Chinese families with at least one member diagnosed with USH. Blood was collected at Peking Union Medical College Hospital. This cohort is one of the largest USH cohorts reported. We utilized customized panel and whole exome sequencing, variant analysis, Sanger validation and segregation tests to find disease causing mutations in these families.

We identified biallelic disease causing mutations in known USH genes in 70 % (49) of our patients. As has been previously reported, MYO7A is the most frequently mutated gene in our USH type I patients while USH2A is the most mutated gene in our USH type II patients. In addition, we identify mutations in CLRN1, DFNB31, GPR98 and PCDH15 for the first time in Chinese USH patients. Together, mutations in CLRN1, DNFB31, GPR98 and PCDH15 account for 11.4 % of disease in our cohort. Interestingly, although the spectrum of disease genes is quite similar between our Chinese patient cohort and other patient cohorts from different (and primarily Caucasian) ethnic backgrounds, the mutations themselves are dramatically different. In particular, 76 % (52/68) of alleles found in this study have never been previously reported. Interestingly, we observed a strong enrichment for severe protein truncating mutations expected to have severe functional consequence on the protein in USH II patients compared to the reported mutation spectrum in RP patients, who often carry partial protein truncating mutations.

Our study provides the first comprehensive genetic characterization of a large collection of Chinese USH patients. Up to 90 % of USH patients have disease caused by mutations in known USH disease genes. By combining NGS-based molecular diagnosis and patient clinical information, a more accurate diagnosis, prognosis and personalized treatment of USH patients can be achieved.

The online version of this article (doi:10.1186/s13023-015-0329-3) contains supplementary material, which is available to authorized users.

• Databases, Genetic
• Diarrhea/microbiology
• Diarrhea/virology
• Humans
• Polymorphism, Genetic/genetics

• GENETICS
• OTOLARYNGOLOGY

• Base Sequence
• DNA
• Genotype
• Hearing
• Hearing Loss/etiology
• Hearing Loss/genetics
• Hearing Loss, Central/etiology
• Hearing Loss, Central/genetics
• Humans
• Mutation
• Phenotype
• Polymorphism, Genetic
• Sequence Analysis, DNA
• Syndrome

Usher syndrome is an autosomal recessive disease characterized by sensorineural hearing loss, age-dependent retinitis pigmentosa (RP), and occasionally vestibular dysfunction. The most severe form is Usher syndrome type 1 (USH1). Mutations in the MYO7A gene are responsible for USH1 and account for 29–55% of USH1 cases. Here, we characterized a Chinese family (no. 7162) with USH1. Combining the targeted capture of 131 known deafness genes, next-generation sequencing, and bioinformatic analysis, we identified two deleterious compound heterozygous mutations in the MYO7A gene: a reported missense mutation c.73G>A (p.G25R) and a novel nonsense mutation c.462C>A (p.C154X). The two compound variants are absent in 219 ethnicity-matched controls, co-segregates with the USH clinical phenotypes, including hearing loss, vestibular dysfunction, and age-dependent penetrance of progressive RP, in family 7162. Therefore, we concluded that the USH1 in this family was caused by compound heterozygous mutations in MYO7A.

• Amino Acid Sequence
• Animals
• China
• Female
• Heterozygote
• Humans
• Male
• Middle Aged
• Molecular Sequence Data
• Mutation
• Myosin VIIa
• Myosins/chemistry
• Myosins/genetics
• Pedigree
• Sequence Homology, Amino Acid
• Usher Syndromes/genetics

• R03 AA020101 NIAAA NIH HHS
• R33 DC010476 NIDCD NIH HHS

Usher syndrome is an autosomal recessive disorder characterized both by deafness and blindness. For the three clinical subtypes of Usher syndrome causal mutations in altogether 12 genes and a modifier gene have been identified. Due to the genetic heterogeneity of Usher syndrome, the molecular analysis is predestined for a comprehensive and parallelized analysis of all known genes by next-generation sequencing (NGS) approaches. We describe here the targeted enrichment and deep sequencing for exons of Usher genes and compare the costs and workload of this approach compared to Sanger sequencing. We also present a bioinformatics analysis pipeline that allows us to detect single-nucleotide variants, short insertions and deletions, as well as copy number variations of one or more exons on the same sequence data. Additionally, we present a flexible in silico gene panel for the analysis of sequence variants, in which newly identified genes can easily be included. We applied this approach to a cohort of 44 Usher patients and detected biallelic pathogenic mutations in 35 individuals and monoallelic mutations in eight individuals of our cohort. Thirty-nine of the sequence variants, including two heterozygous deletions comprising several exons of USH2A, have not been reported so far. Our NGS-based approach allowed us to assess single-nucleotide variants, small indels, and whole exon deletions in a single test. The described diagnostic approach is fast and cost-effective with a high molecular diagnostic yield.

• Gene panel diagnostics
• Usher syndrome
• next-generation sequencing

Usher syndrome (USH) is an autosomal recessive disorder comprising retinitis pigmentosa, hearing loss and, in some cases, vestibular dysfunction. It is clinically and genetically heterogeneous with three distinctive clinical types (I–III) and nine Usher genes identified. This study is a comprehensive clinical and genetic analysis of 172 Usher patients and evaluates the contribution of digenic inheritance.

The genes MYO7A, USH1C, CDH23, PCDH15, USH1G, USH2A, GPR98, WHRN, CLRN1 and the candidate gene SLC4A7 were sequenced in 172 UK Usher patients, regardless of clinical type.

No subject had definite mutations (nonsense, frameshift or consensus splice site mutations) in two different USH genes. Novel missense variants were classified UV1-4 (unclassified variant): UV4 is ‘probably pathogenic’, based on control frequency <0.23%, identification in trans to a pathogenic/probably pathogenic mutation and segregation with USH in only one family; and UV3 (‘likely pathogenic’) as above, but no information on phase. Overall 79% of identified pathogenic/UV4/UV3 variants were truncating and 21% were missense changes. MYO7A accounted for 53.2%, and USH1C for 14.9% of USH1 families (USH1C:c.496+1G>A being the most common USH1 mutation in the cohort). USH2A was responsible for 79.3% of USH2 families and GPR98 for only 6.6%. No mutations were found in USH1G, WHRN or SLC4A7.

One or two pathogenic/likely pathogenic variants were identified in 86% of cases. No convincing cases of digenic inheritance were found. It is concluded that digenic inheritance does not make a significant contribution to Usher syndrome; the observation of multiple variants in different genes is likely to reflect polymorphic variation, rather than digenic effects.

Usher Syndrome type II (USH2) is an autosomal recessive disorder, characterized by moderate to severe hearing impairment and retinitis pigmentosa (RP). Among the three genes implicated, mutations in the USH2A gene account for 74-90% of the USH2 cases.

To identify the genetic cause of the disease and determine the frequency of USH2A mutations in a cohort of 88 unrelated USH Spanish patients, we carried out a mutation screening of the 72 coding exons of this gene by direct sequencing. Moreover, we performed functional minigene studies for those changes that were predicted to affect splicing.

As a result, a total of 144 DNA sequence variants were identified. Based upon previous studies, allele frequencies, segregation analysis, bioinformatics' predictions and in vitro experiments, 37 variants (23 of them novel) were classified as pathogenic mutations.

This report provide a wide spectrum of USH2A mutations and clinical features, including atypical Usher syndrome phenotypes resembling Usher syndrome type I. Considering only the patients clearly diagnosed with Usher syndrome type II, and results obtained in this and previous studies, we can state that mutations in USH2A are responsible for 76.1% of USH2 disease in patients of Spanish origin.

• Adaptor Proteins, Signal Transducing/genetics
• Adult
• Cell Cycle Proteins
• Cytoskeletal Proteins
• Female
• Hearing Loss, Sensorineural/diagnosis
• Hearing Loss, Sensorineural/genetics
• Humans
• Male
• Mutation
• Ophthalmoscopy
• Pedigree
• Phenotype
• Retinitis Pigmentosa/diagnosis
• Retinitis Pigmentosa/genetics
• Sequence Analysis, DNA
• Siblings
• Tomography, Optical Coherence
• Vestibular Function Tests
• Visual Acuity

• G0300212 Medical Research Council
• Wellcome Trust

• Adaptor Proteins, Signal Transducing/genetics
• Animals
• Cell Cycle Proteins
• Cells, Cultured
• Codon, Nonsense/drug effects
• Cytoskeletal Proteins
• Electroporation
• Genetic Vectors/genetics
• Gentamicins/pharmacology
• Humans
• Luminescent Proteins
• Mice
• Mice, Inbred C57BL
• Microscopy, Fluorescence
• Oxadiazoles/pharmacology
• Oxadiazoles/therapeutic use
• Retina/cytology
• Retina/pathology
• Usher Syndromes/drug therapy
• Usher Syndromes/genetics
• Usher Syndromes/pathology
• Red Fluorescent Protein

• Algorithms
• Alternative Splicing
• Base Sequence
• DNA Mutational Analysis
• Exons
• Gene Expression Profiling
• Gene Expression Regulation
• HeLa Cells
• Humans
• Introns
• Models, Genetic
• Molecular Sequence Data
• Mutation
• Structure-Activity Relationship
• Usher Syndromes/genetics

• usher syndrome
• retinitis pigmentosa
• mutation
• deafness

• Cohort Studies
• Computational Biology/methods
• Extracellular Matrix Proteins/genetics
• Genetic Predisposition to Disease/genetics
• Humans
• Mutation
• Mutation, Missense/genetics
• Protein Isoforms/genetics
• Retinitis Pigmentosa
• Sequence Analysis, DNA/methods
• Usher Syndromes/genetics

• P30-EY014104 NEI NIH HHS
• R01 EY000169 NEI NIH HHS
• R01 EY008683 NEI NIH HHS
• NIH-EY08683 NEI NIH HHS
• NIH-EY00169 NEI NIH HHS
• P30 EY014104 NEI NIH HHS
• R37 EY000169 NEI NIH HHS

• Animals
• Binding Sites
• Cadherin Related Proteins
• Cadherins/chemistry
• Cadherins/metabolism
• Deafness/metabolism
• Deafness/physiopathology
• Hair Cells, Auditory/metabolism
• Hearing/physiology
• Mechanotransduction, Cellular/physiology
• Mice
• Models, Molecular
• Protein Conformation
• Protein Precursors/chemistry
• Protein Precursors/metabolism
• Structure-Activity Relationship

• R01 DC002281 NIDCD NIH HHS
• R01 DC02281 NIDCD NIH HHS
• P41 RR015301 NCRR NIH HHS
• RR-15301 NCRR NIH HHS
• Howard Hughes Medical Institute