Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

ObjectiveTo evaluate the use of new genetic sequencing techniques for comprehensive genetic testing for hearing loss.Data SourcesArticles were identified from PubMed and Google Scholar databases using pertinent search terms.Review MethodsLiterature search identified 30 studies as candidates that met search criteria. Three studies were excluded, and 8 studies were found to be case reports. Twenty studies were included for review analysis, including 7 studies that evaluated controls and 16 studies that evaluated patients with unknown causes of hearing loss; 3 studies evaluated both controls and patients.ConclusionsIn the 20 studies included in the review analysis, 426 control samples and 603 patients with unknown causes of hearing loss underwent comprehensive genetic diagnosis for hearing loss using massively parallel sequencing. Control analysis showed a sensitivity and specificity >99%, sufficient for clinical use of these tests. The overall diagnostic rate was 41% (range, 10%-83%) and varied based on sev...

/pdf/massively-parallel-sequencing-for-genetic-diagnosis-of-c3wsdllvt7.pdf

Massively Parallel Sequencing for Genetic Diagnosis of Hearing Loss: The New Standard of Care

Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.

/pdf/spectrum-of-dna-variants-for-non-syndromic-deafness-in-a-1vjyzxw18h.pdf

Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents

Usher syndrome has three subtypes, each being clinically and genetically heterogeneous characterised by sensorineural hearing loss and retinitis pigmentosa (RP), with or without vestibular dysfunct...

Usher syndrome: clinical features, molecular genetics and advancing therapeutics.

Objective:To describe the genetic and phenotypic spectrum of Usher syndrome after 6 years of studies by next-generation sequencing, and propose an up-to-date classification of Usher genes in patients with both visual and hearing impairments suggesting Usher syndrome, and in patients with seemingly i

Genetics of Usher Syndrome: New Insights From a Meta-analysis.

Although over 60 non-syndromic deafness genes have been identified to date, the etiologic contribution of most deafness genes remained elusive. In this study, we addressed this issue by targeted next-generation sequencing of a large cohort of non-syndromic deaf probands. Probands with mutations in commonly screened deafness genes GJB2, SLC26A4 and MT-RNR1 were pre-excluded by Sanger sequencing. The remaining 125 deaf probands proceeded through targeted exon capturing of 79 known deafness genes and Illumina HiSeq2000 sequencing. Bi-allelic mutations in 15 less commonly screened deafness genes were identified in 28 deaf probands, with mutations in MYO15A, GPR98, TMC1, USH2A and PCDH15 being relatively more frequent (≥3 probands each). Dominant mutations in MYO6, TECTA, POU4F3 and COCH were identified in 4 deaf families. A mitochondrial MTTS1 mutation was identified in one maternally inherited deaf family. No pathogenic mutations were identified in three dominant deaf families and two consanguineous families. Mutations in the less commonly screened deafness genes were heterogeneous and contributed to a significant percentage (17.4%) of causes for non-syndromic deafness. Targeted next-generation sequencing provided a comprehensive and efficient diagnosis for known deafness genes. Complementary to linkage analysis or whole-exome sequencing of deaf families, pre-exclusion of known deafness genes by this strategy may facilitate the discovery of novel deafness genes.

/pdf/genetic-etiology-study-of-the-non-syndromic-deafness-in-28dk39thvb.pdf

Genetic etiology study of the non-syndromic deafness in Chinese Hans by targeted next-generation sequencing.

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Genetic etiology study of the non-syndromic deafness in Chinese Hans by targeted next-generation sequencing.