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Reda Del Barrio S, García Fernández A, Quesada-Espinosa JF, Sánchez-Calvín MT, Gómez-Manjón I, Sierra-Tomillo O, Juárez-Rufián A, de Vergas Gutiérrez J. Genetic diagnosis of childhood sensorineural hearing loss. ACTA OTORRINOLARINGOLOGICA ESPANOLA 2024; 75:83-93. [PMID: 38224868 DOI: 10.1016/j.otoeng.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/03/2023] [Indexed: 01/17/2024]
Abstract
INTRODUCTION Congenital/early-onset sensorineural hearing loss (SNHL) is one of the most common hereditary disorders in our environment. There is increasing awareness of the importance of an etiologic diagnosis, and genetic testing with next-generation sequencing (NGS) has the highest diagnostic yield. Our study shows the genetic results obtained in a cohort of patients with bilateral congenital/early-onset SNHL. MATERIALS AND METHODS We included 105 children with bilateral SNHL that received genetic testing between 2019 and 2022. Genetic tests were performed with whole exome sequencing, analyzing genes related to hearing loss (virtual panel with 244 genes). RESULTS 48% (50/105) of patients were genetically diagnosed. We identified pathogenic and likely pathogenic variants in 26 different genes, and the most frequently mutated genes were GJB2, USH2A and STRC. 52% (26/50) of variants identified produced non-syndromic hearing loss, 40% (20/50) produced syndromic hearing loss, and the resting 8% (4/50) could produce both non-syndromic and syndromic hearing loss. CONCLUSIONS Genetic testing plays a vital role in the etiologic diagnosis of bilateral SNHL. Our cohort shows that genetic testing with NGS has a high diagnostic yield and can provide useful information for the clinical workup of patients.
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Affiliation(s)
- Sara Reda Del Barrio
- Servicio de Otorrinolaringología, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | | | | | | | - Irene Gómez-Manjón
- Servicio de Genética, Hospital Universitario 12 de Octubre, Madrid, Spain
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Tisi A, Palaniappan S, Maccarrone M. Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease. Biomolecules 2023; 13:1534. [PMID: 37892216 PMCID: PMC10605747 DOI: 10.3390/biom13101534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.
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Affiliation(s)
- Annamaria Tisi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Sakthimala Palaniappan
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Laboratory of Lipid Neurochemistry, European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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Liu C, Huang Y, Zhang Y, Ding H, Yu L, Wang A, Wang Y, Zeng Y, Liu L, Liu Y, Qi Y, Li F, Wu J, Du L, Mai F, Zhang Q, Wang X, Yin A. Next-generation sequencing facilitates genetic diagnosis and improves the management of patients with hearing loss in clinical practice. Int J Pediatr Otorhinolaryngol 2022; 161:111258. [PMID: 35939872 DOI: 10.1016/j.ijporl.2022.111258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 07/13/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Hearing loss (HL) is a prevalent sensorineural disorder, and is among the most etiologically heterogeneous disorders. With the advent of next-generation sequencing (NGS) technologies, hundreds of candidate genes can be analyzed simultaneously in a cost-effective manner. METHODS Ninety-four patients from 87 families diagnosed with non-syndromic or syndromic HL were enrolled. A custom-designed HL panel and clinical exome sequencing (CES) were applied to explore molecular etiology in the cohort, and the efficacy of the two panels was examined. RESULTS The etiologic diagnosis for HL has been identified for 36 out of 87 probands (41.4%), 28 with an autosomal recessive (AR) inheritance pattern and 8 with an autosomal dominant (AD) pattern. Candidate variants in 18 different genes were identified in the study cohort, 10 with AR inheritance pattern and 8 with AD pattern. Fourteen of the variants identified in the study were novel. CONCLUSIONS The custom-designed HL panel covers almost all known HL-associated genes, and can be used as an effective clinical diagnostic platform; CES evaluates all exons related to clinical symptoms, and is also suitable for clinical diagnosis of HL. Next-generation sequencing facilitates genetic diagnosis and improves the management of patients with HL in the clinical practice.
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Affiliation(s)
- Chang Liu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Yanlin Huang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Yan Zhang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Hongke Ding
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Lihua Yu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Anshi Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Yunan Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Yukun Zeng
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Ling Liu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Yuan Liu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Fake Li
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Jing Wu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Li Du
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Fei Mai
- Department of ENT, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Qi Zhang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Xingwang Wang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China; Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong, 510010, China.
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Han S, Zhang D, Guo Y, Fu Z, Guan G. Prevalence and Characteristics of STRC Gene Mutations (DFNB16): A Systematic Review and Meta-Analysis. Front Genet 2021; 12:707845. [PMID: 34621290 PMCID: PMC8491653 DOI: 10.3389/fgene.2021.707845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Mutations in the STRC (MIM 606440) gene, inducing DFNB16, are considered a major cause of mild–moderate autosomal recessive non-syndromic hearing loss (ARNSHL). We conducted a systematic review and meta-analysis to determine the global prevalence and characteristics of STRC variations, important information required for genetic counseling. Methods: PubMed, Google Scholar, Medline, Embase, and Web of Science were searched for relevant articles published before January 2021. Results: The pooled prevalence of DFNB16 in GJB2-negative patients with hearing loss was 4.08% (95% CI: 0.0289–0.0573), and the proportion of STRC variants in the mild–moderate hearing loss group was 14.36%. Monoallelic mutations of STRC were 4.84% (95% CI: 0.0343–0.0680) in patients with deafness (non-GJB2) and 1.36% (95% CI: 0.0025–0.0696) in people with normal hearing. The DFNB16 prevalence in genetically confirmed patients (non-GJB2) was 11.10% (95% CI: 0.0716–0.1682). Overall pooled prevalence of deafness–infertility syndrome (DIS) was 36.75% (95% CI: 0.2122–0.5563) in DFNB16. The prevalence of biallelic deletions in STRC gene mutations was 70.85% (95% CI: 0.5824–0.8213). Conclusion: Variants in the STRC gene significantly contribute to mild–moderate hearing impairment. Moreover, biallelic deletions are a main feature of STRC mutations. Copy number variations associated with infertility should be seriously considered when investigating DFNB16.
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Affiliation(s)
- Shuang Han
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yingyuan Guo
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Zeming Fu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Guofang Guan
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun, China
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