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Justin Margret J, Jayasankaran C, Amritkumar P, Azaiez H, Srisailapathy CRS. Unraveling the Genetic Basis of Combined Deafness and Male Infertility Phenotypes through High-Throughput Sequencing in a Unique Cohort from South India. ADVANCED GENETICS (HOBOKEN, N.J.) 2024; 5:2300206. [PMID: 38884051 PMCID: PMC11170077 DOI: 10.1002/ggn2.202300206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/15/2024] [Indexed: 06/18/2024]
Abstract
The co-occurrence of sensorineural hearing loss and male infertility has been reported in several instances, suggesting potential shared genetic underpinnings. One such example is the contiguous gene deletion of CATSPER2 and STRC genes, previously associated with deafness-infertility syndrome (DIS) in males. Fifteen males with both hearing loss and infertility from southern India after exclusion for the DIS contiguous gene deletion and the FOXI1 gene mutations are subjected to exome sequencing. This resolves the genetic etiology in four probands for both the phenotypes; In the remaining 11 probands, two each conclusively accounted for deafness and male infertility etiologies. Genetic heterogeneity is well reflected in both phenotypes. Four recessive (TRIOBP, SLC26A4, GJB2, COL4A3) and one dominant (SOX10) for the deafness; six recessive genes (LRGUK, DNAH9, ARMC4, DNAH2, RSPH6A, and ACE) for male infertility can be conclusively ascribed. LRGUK and RSPH6A genes are implicated earlier only in mice models, while the ARMC4 gene is implicated in chronic destructive airway diseases due to primary ciliary dyskinesia. This study would be the first to document the role of these genes in the male infertility phenotype in humans. The result suggests that deafness and infertility are independent events and do not segregate together among the probands.
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Affiliation(s)
- Jeffrey Justin Margret
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Department of Pediatrics Louisiana State University Health Sciences Center Shreveport LA 71103 USA
| | - Chandru Jayasankaran
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Department of Personalized Health Care Roche Products India Pvt., Ltd. Bengaluru Karnataka 560 025 India
| | - Pavithra Amritkumar
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
- Meenakshi Academy of Higher Education and Research (MAHER) Chennai 600 078 India
| | - Hela Azaiez
- Department of Otolaryngology Carver College of Medicine University of Iowa Iowa City Iowa 52242 USA
| | - C R Srikumari Srisailapathy
- Department of Genetics Dr. ALM Post Graduate Institute of Basic Medical Sciences University of Madras Taramani Campus Chennai 600 113 India
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2
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Peart L, Tekin M. Genetic Landscape of Hearing Loss in the Caribbean: A Narrative Review. Balkan Med J 2024; 41:161-166. [PMID: 38700265 PMCID: PMC11077928 DOI: 10.4274/balkanmedj.galenos.2024.2024-2-110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/15/2024] [Indexed: 05/05/2024] Open
Abstract
The Caribbean region has a diverse population of about 40 million people, spread over 13 sovereign states. This review aims to describe the existing studies on hereditary hearing loss (HL) in the Caribbean population. We systematically reviewed scientific articles on HL prevalence, genetic causes, technology use, and environmental effects in Caribbean nations and the Caribbean diaspora in the United States. Key findings show that HL rates, with diverse genetic variables, vary across Puerto Rico, Cuba, and the Dominican Republic. Local resources and technology have been used to diagnose HL, particularly in rural areas. Environmental factors tend to affect HL prevalence in various regions. This literature review of Caribbean-focused studies helps guide future research and healthcare strategies, particularly concerning genetic drift caused by migration to the United States. Understanding these factors can help diagnose and treat HL in America's diverse population.
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Affiliation(s)
- LéShon Peart
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
- John P. Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
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3
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Hu SW, Lv J, Wang Z, Tang H, Wang H, Wang F, Wang D, Zhang J, Zhang L, Cao Q, Chen Y, Gao Z, Han Y, Wang W, Li GL, Shu Y, Li H. Engineering of the AAV-Compatible Hair Cell-Specific Small-Size Myo15 Promoter for Gene Therapy in the Inner Ear. RESEARCH (WASHINGTON, D.C.) 2024; 7:0341. [PMID: 38665848 PMCID: PMC11045262 DOI: 10.34133/research.0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/21/2024] [Indexed: 04/28/2024]
Abstract
Adeno-associated virus (AAV)-mediated gene therapy is widely applied to treat numerous hereditary diseases in animal models and humans. The specific expression of AAV-delivered transgenes driven by cell type-specific promoters should further increase the safety of gene therapy. However, current methods for screening cell type-specific promoters are labor-intensive and time-consuming. Herein, we designed a "multiple vectors in one AAV" strategy for promoter construction in vivo. Through this strategy, we truncated a native promoter for Myo15 expression in hair cells (HCs) in the inner ear, from 1,611 bp down to 1,157 bp, and further down to 956 bp. Under the control of these 2 promoters, green fluorescent protein packaged in AAV-PHP.eB was exclusively expressed in the HCs. The transcription initiation ability of the 2 promoters was further verified by intein-mediated otoferlin recombination in a dual-AAV therapeutic system. Driven by these 2 promoters, human otoferlin was selectively expressed in HCs, resulting in the restoration of hearing in treated Otof -/- mice for at least 52 weeks. In summary, we developed an efficient screening strategy for cell type-specific promoter engineering and created 2 truncated Myo15 promoters that not only restored hereditary deafness in animal models but also show great potential for treating human patients in future.
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Affiliation(s)
- Shao Wei Hu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Jun Lv
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Zijing Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Honghai Tang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Hui Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Fang Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Daqi Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Juan Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Longlong Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Qi Cao
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yuxin Chen
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Ziwen Gao
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yu Han
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Wuqing Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Geng-lin Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yilai Shu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Huawei Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
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4
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Almalki F. Review and research gap identification in genetics causes of syndromic and nonsyndromic hearing loss in Saudi Arabia. Ann Hum Genet 2024. [PMID: 38517009 DOI: 10.1111/ahg.12559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/13/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
Abstract
Congenital hearing loss is one of the most common sensory disabilities worldwide. The genetic causes of hearing loss account for 50% of hearing loss. Genetic causes of hearing loss can be classified as nonsyndromic hearing loss (NSHL) or syndromic hearing loss (SHL). NSHL is defined as a partial or complete hearing loss without additional phenotypes; however, SHL, known as hearing loss, is associated with other phenotypes. Both types follow a simple Mendelian inheritance fashion. Several studies have been conducted to uncover the genetic factors contributing to NSHL and SHL in Saudi patients. However, these studies have encountered certain limitations. This review assesses and discusses the genetic factors underpinning NSHL and SHL globally, with a specific emphasis on the Saudi Arabian context. It also explores the prevalence of the most observed genetic causes of NSHL and SHL in Saudi Arabia. It also sheds light on areas where further research is needed to fully understand the genetic foundations of hearing loss in the Saudi population. This review identifies several gaps in research in NSHL and SHL and provides insights into potential research to be conducted.
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Affiliation(s)
- Faisal Almalki
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Al Madinah Al Munwarah, Saudi Arabia
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5
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Ali A, Tabouni M, Kizhakkedath P, Baydoun I, Allam M, John A, Busafared F, Alnuaimi A, Al-Jasmi F, Alblooshi H. Spectrum of genetic variants in bilateral sensorineural hearing loss. Front Genet 2024; 15:1314535. [PMID: 38410152 PMCID: PMC10894970 DOI: 10.3389/fgene.2024.1314535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024] Open
Abstract
Background: Hearing loss (HL) is an impairment of auditory function with identified genetic forms that can be syndromic (30%) or non-syndromic (70%). HL is genetically heterogeneous, with more than 1,000 variants across 150 causative genes identified to date. The genetic diagnostic rate varies significantly depending on the population being tested. Countries with a considerably high rate of consanguinity provide a unique resource for studying rare forms of recessive HL. In this study, we identified genetic variants associated with bilateral sensorineural HL (SNHL) using whole-exome sequencing (WES) in 11 families residing in the United Arab Emirates (UAE). Results: We established the molecular diagnosis in six probands, with six different pathogenic or likely pathogenic variants in the genes MYO15A, SLC26A4, and GJB2. One novel nonsense variant, MYO15A:p.Tyr1962Ter*, was identified in a homozygous state in one family, which has not been reported in any public database. SLC26A4 and GJB2 were found to be the most frequently associated genes in this study. In addition, six variants of uncertain significance (VUS) were detected in five probands in the genes CDH23, COL11A1, ADGRV1, NLRP3, and GDF6. In total, 12 variants were observed in eight genes. Among these variants, eight missense variants (66.7%), three nonsense variants (25.0%), and one frameshift (8.3%) were identified. The overall diagnostic rate of this study was 54.5%. Approximately 45.5% of the patients in this study came from consanguineous families. Conclusion: Understanding the genetic basis of HL provides insight for the clinical diagnosis of hearing impairment cases through the utilization of next-generation sequencing (NGS). Our findings contribute to the knowledge of the heterogeneous genetic profile of HL, especially in a population with a high rate of consanguineous marriage in the Arab population.
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Affiliation(s)
- Amanat Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Tabouni
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Praseetha Kizhakkedath
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ibrahim Baydoun
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anne John
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Faiza Busafared
- Department of Otolaryngology, Al Kuwait Hospital, Dubai, United Arab Emirates
| | - Ayesha Alnuaimi
- Department of Otolaryngology, Al Kuwait Hospital, Dubai, United Arab Emirates
| | - Fatma Al-Jasmi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Hiba Alblooshi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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6
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Fehrmann MLA, Huinck WJ, Thijssen MEG, Haer-Wigman L, Yntema HG, Rotteveel LJC, Widdershoven JCC, Goderie T, van Dooren MF, Hoefsloot EH, van der Schroeff MP, Mylanus EAM, Lanting CP, Pennings RJE. Stable long-term outcomes after cochlear implantation in subjects with TMPRSS3 associated hearing loss: a retrospective multicentre study. J Otolaryngol Head Neck Surg 2023; 52:82. [PMID: 38102706 PMCID: PMC10724910 DOI: 10.1186/s40463-023-00680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/06/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND The spiral ganglion hypothesis suggests that pathogenic variants in genes preferentially expressed in the spiral ganglion nerves (SGN), may lead to poor cochlear implant (CI) performance. It was long thought that TMPRSS3 was particularly expressed in the SGNs. However, this is not in line with recent reviews evaluating CI performance in subjects with TMPRSS3-associated sensorineural hearing loss (SNHL) reporting overall beneficial outcomes. These outcomes are, however, based on variable follow-up times of, in general, 1 year or less. Therefore, we aimed to 1. evaluate long-term outcomes after CI implantation of speech recognition in quiet in subjects with TMPRSS3-associated SNHL, and 2. test the spiral ganglion hypothesis using the TMPRSS3-group. METHODS This retrospective, multicentre study evaluated long-term CI performance in a Dutch population with TMPRSS3-associated SNHL. The phoneme scores at 70 dB with CI in the TMPRSS3-group were compared to a control group of fully genotyped cochlear implant users with post-lingual SNHL without genes affecting the SGN, or severe anatomical inner ear malformations. CI-recipients with a phoneme score ≤ 70% at least 1-year post-implantation were considered poor performers and were evaluated in more detail. RESULTS The TMPRSS3 group consisted of 29 subjects (N = 33 ears), and the control group of 62 subjects (N = 67 ears). For the TMPRSS3-group, we found an average phoneme score of 89% after 5 years, which remained stable up to 10 years post-implantation. At both 5 and 10-year follow-up, no difference was found in speech recognition in quiet between both groups (p = 0.830 and p = 0.987, respectively). Despite these overall adequate CI outcomes, six CI recipients had a phoneme score of ≤ 70% and were considered poor performers. The latter was observed in subjects with residual hearing post-implantation or older age at implantation. CONCLUSION Subjects with TMPRSS3-associated SNHL have adequate and stable long-term outcomes after cochlear implantation, equal to the performance of genotyped patient with affected genes not expressed in the SGN. These findings are not in line with the spiral ganglion hypothesis. However, more recent studies showed that TMPRSS3 is mainly expressed in the hair cells with only limited SGN expression. Therefore, we cannot confirm nor refute the spiral ganglion hypothesis.
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Affiliation(s)
- M L A Fehrmann
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - W J Huinck
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - M E G Thijssen
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - L Haer-Wigman
- Department of Clinical Genetics, Radboudumc, Nijmegen, The Netherlands
| | - H G Yntema
- Department of Clinical Genetics, Radboudumc, Nijmegen, The Netherlands
| | - L J C Rotteveel
- Department of Otorhinolaryngology, Leiden UMC, Leiden, The Netherlands
| | - J C C Widdershoven
- Department of Otorhinolaryngology, Maastricht UMC, Maastricht, The Netherlands
| | - T Goderie
- Department of Otorhinolaryngology-Head and Neck Surgery, Ear and Hearing, Amsterdam UMC, Amsterdam, The Netherlands
| | - M F van Dooren
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - E H Hoefsloot
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - E A M Mylanus
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - C P Lanting
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands
| | - R J E Pennings
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, The Netherlands.
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7
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Peart L, Gonzalez J, Morel Swols D, Duman D, Saridogan T, Ramzan M, Zafeer MF, Liu XZ, Eshraghi AA, Hoffer ME, Angeli SI, Bademci G, Blanton S, Smith C, Telischi FF, Tekin M. Dispersed DNA variants underlie hearing loss in South Florida's minority population. Hum Genomics 2023; 17:103. [PMID: 37996878 PMCID: PMC10668374 DOI: 10.1186/s40246-023-00556-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 11/19/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND We analyzed the genetic causes of sensorineural hearing loss in racial and ethnic minorities of South Florida by reviewing demographic, phenotypic, and genetic data on 136 patients presenting to the Hereditary Hearing Loss Clinic at the University of Miami. In our retrospective chart review, of these patients, half self-identified as Hispanic, and the self-identified racial distribution was 115 (86%) White, 15 (11%) Black, and 6 (4%) Asian. Our analysis helps to reduce the gap in understanding the prevalence, impact, and genetic factors related to hearing loss among diverse populations. RESULTS The causative gene variant or variants were identified in 54 (40%) patients, with no significant difference in the molecular diagnostic rate between Hispanics and Non-Hispanics. However, the total solve rate based on race was 40%, 47%, and 17% in Whites, Blacks, and Asians, respectively. In Non-Hispanic Whites, 16 different variants were identified in 13 genes, with GJB2 (32%), MYO7A (11%), and SLC26A4 (11%) being the most frequently implicated genes. In White Hispanics, 34 variants were identified in 20 genes, with GJB2 (22%), MYO7A (7%), and STRC-CATSPER2 (7%) being the most common. In the Non-Hispanic Black cohort, the gene distribution was evenly dispersed, with 11 variants occurring in 7 genes, and no variant was identified in 3 Hispanic Black probands. For the Asian cohort, only one gene variant was found out of 6 patients. CONCLUSION This study demonstrates that the diagnostic rate of genetic studies in hearing loss varies according to race in South Florida, with more heterogeneity in racial and ethnic minorities. Further studies to delineate deafness gene variants in underrepresented populations, such as African Americans/Blacks from Hispanic groups, are much needed to reduce racial and ethnic disparities in genetic diagnoses.
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Affiliation(s)
- LéShon Peart
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Joanna Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Dayna Morel Swols
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Duygu Duman
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Audiology, Faculty of Health Sciences, Ankara University, Ankara, Turkey
| | - Turcin Saridogan
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Memoona Ramzan
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Mohammad Faraz Zafeer
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Xue Zhong Liu
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Adrien A Eshraghi
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Michael E Hoffer
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Simon I Angeli
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Guney Bademci
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan Blanton
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Carson Smith
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Fred F Telischi
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Mustafa Tekin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
- Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, FL, USA.
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8
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Lee S, Yun Y, Cha JH, Han JH, Lee DH, Song JJ, Park MK, Lee JH, Oh SH, Choi BY, Lee SY. Phenotypic and molecular basis of SIX1 variants linked to non-syndromic deafness and atypical branchio-otic syndrome in South Korea. Sci Rep 2023; 13:11776. [PMID: 37479820 PMCID: PMC10361970 DOI: 10.1038/s41598-023-38909-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Branchio-oto-renal (BOR)/branchio-otic (BO) syndrome is a rare disorder and exhibits clinically heterogenous phenotypes, marked by abnormalities in the ear, branchial arch, and renal system. Sporadic cases of atypical BOR/BO syndrome have been recently reported; however, evidence on genotype-phenotype correlations and molecular mechanisms of those cases is lacking. We herein identified five SIX1 heterozygous variants (c.307dupC:p.Leu103Profs*51, c.373G>A:p.Glu125Lys, c.386_391del:p.Tyr129_Cys130del, c.397_399del:p.Glu133del, and c.501G>C:p.Gln167His), including three novel variants, through whole-exome sequencing in five unrelated Korean families. All eight affected individuals with SIX1 variants displayed non-syndromic hearing loss (DFNA23) or atypical BO syndrome. The prevalence of major and minor criteria for BOR/BO syndrome was significantly reduced among individuals with SIX1 variants, compared to 15 BOR/BO syndrome families with EYA1 variants. All SIX1 variants interacted with the EYA1 wild-type; their complexes were localized in the nucleus except for the p.Leu103Profs*51 variant. All mutants also showed obvious but varying degrees of reduction in DNA binding affinity, leading to a significant decrease in transcriptional activity. This study presents the first report of SIX1 variants in South Korea, expanding the genotypic and phenotypic spectrum of SIX1 variants, characterized by DFNA23 or atypical BO syndrome, and refines the diverse molecular aspects of SIX1 variants according to the EYA1-SIX1-DNA complex theory.
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Affiliation(s)
- Somin Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Yejin Yun
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ju Hyuen Cha
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul, South Korea
| | - Dae Hee Lee
- CTCELLS, Inc., 21, Yuseong-Daero, 1205 Beon-Gil, Yuseong-Gu, Daejeon, Republic of Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul, South Korea
| | - Moo Kyun Park
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul, South Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.
- Department of Genomic Medicine, Precision Medicine & Rare Disease Center, Seoul National University Hospital, Jongno-Gu, Daehak-Ro, 101, Seoul, South Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, South Korea.
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9
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Yuan Y, Yan D, Skidmore J, Chapagain P, Liu X, He S. Responsiveness of the electrically stimulated cochlear nerve in patients with a missense variant in ACTG1: Preliminary Results. FRONTIERS IN AUDIOLOGY AND OTOLOGY 2023; 1:1213323. [PMID: 38590973 PMCID: PMC11000624 DOI: 10.3389/fauot.2023.1213323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
This preliminary study identified a missense variant in ACTG1 (NM_001614.5) in a family with autosomal dominant non-syndromic hearing loss (ADNSHL). The responsiveness of the electrically-stimulated cochlear nerve (CN) in two implanted participants with this missense change was also evaluated and reported. Genetic testing was done using a custom capture panel (MiamiOtoGenes) and whole exome sequencing. The responsiveness of the electrically-stimulated CN was evaluated in two members of this family (G1 and G4) using the electrically evoked compound action potential (eCAP). eCAP results from these two participants were compared with those measured three implanted patient populations: children with cochlear nerve deficiency, children with idiopathic hearing loss and normal-sized cochlear nerves, and postligually deafened adults. Sequencing of ACTG1 identified a missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) which is most likely the genetic cause of ADNSHL in this family. eCAP results measured in these two participants showed substantial variations. The results indicated the missense c.737A>T (p. Gln246Leu) variant in ACTG1 (NM_001614.5) co-segregated with hearing loss in this family. The responsiveness of the electrically-stimulated CN can vary among patients with the same genetic variants, which suggests the importance of evaluating the functional status of the CN for individual CI patients.
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Affiliation(s)
- Yi Yuan
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Denise Yan
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Jeffrey Skidmore
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Prem Chapagain
- Department of Physics and Biomolecular Sciences Institute, Florida International University, Miami, Florida, USA
| | - Xuezhong Liu
- Department of Otolaryngology – Head & Neck Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T. MacDonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Shuman He
- Department of Otolaryngology – Head & Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
- Department of Audiology, Nationwide Children’s Hospital, Columbus, Ohio, USA
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10
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Nisenbaum E, Yan D, Shearer AE, de Joya E, Thielhelm T, Russell N, Staecker H, Chen Z, Holt JR, Liu X. Genotype-Phenotype Correlations in TMPRSS3 (DFNB10/DFNB8) with Emphasis on Natural History. Audiol Neurootol 2023; 28:407-419. [PMID: 37331337 PMCID: PMC10857012 DOI: 10.1159/000528766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/20/2022] [Indexed: 06/20/2023] Open
Abstract
BACKGROUND Mutations in TMPRSS3 are an important cause of autosomal recessive non-syndromic hearing loss. The hearing loss associated with mutations in TMPRSS3 is characterized by phenotypic heterogeneity, ranging from mild to profound hearing loss, and is generally progressive. Clinical presentation and natural history of TMPRSS3 mutations vary significantly based on the location and type of mutation in the gene. Understanding these genotype-phenotype relationships and associated natural disease histories is necessary for the successful development and application of gene-based therapies and precision medicine approaches to DFNB8/10. The heterogeneous presentation of TMPRSS3-associated disease makes it difficult to identify patients clinically. As the body of literature on TMPRSS3-associated deafness grows, there is need for better categorization of the hearing phenotypes associated with specific mutations in the gene. SUMMARY In this review, we summarize TMPRSS3 genotype-phenotype relationships including a thorough description of the natural history of patients with TMPRSS3-associated hearing loss to lay the groundwork for the future of TMPRSS3 treatment using molecular therapy. KEY MESSAGES TMPRSS3 mutation is a significant cause of genetic hearing loss. All patients with TMPRSS3 mutation display severe-to-profound prelingual (DFNB10) or a postlingual (DFNB8) progressive sensorineural hearing loss. Importantly, TMPRSS3 mutations have not been associated with middle ear or vestibular deficits. The c.916G>A (p.Ala306Thr) missense mutation is the most frequently reported mutation across populations and should be further explored as a target for molecular therapy.
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Affiliation(s)
- Eric Nisenbaum
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA,
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - A Eliot Shearer
- Department of Otolaryngology-Head and Neck Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Evan de Joya
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Torin Thielhelm
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Nicole Russell
- Department of Otolaryngology-Head and Neck Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hinrich Staecker
- Department of Otolaryngology Head and Neck Surgery, University of Kansas Health System, Kansas City, Kansas, USA
| | - Zhengyi Chen
- Department of Otolaryngology and Program in Neuroscience, Harvard Medical School and Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Jeffrey R Holt
- Department of Otolaryngology-Head and Neck Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- Department of Otolaryngology and Program in Neuroscience, Harvard Medical School and Eaton Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida, USA
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11
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Asaad M, Mahfood M, Al Mutery A, Tlili A. Loss-of-function mutations in MYO15A and OTOF cause non-syndromic hearing loss in two Yemeni families. Hum Genomics 2023; 17:42. [PMID: 37189200 DOI: 10.1186/s40246-023-00489-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Hearing loss is a rare hereditary deficit that is rather common among consanguineous populations. Autosomal recessive non-syndromic hearing loss is the predominant form of hearing loss worldwide. Although prevalent, hearing loss is extremely heterogeneous and poses a pitfall in terms of diagnosis and screening. Using next-generation sequencing has enabled a rapid increase in the identification rate of genes and variants in heterogeneous conditions, including hearing loss. We aimed to identify the causative variants in two consanguineous Yemeni families affected with hearing loss using targeted next-generation sequencing (clinical exome sequencing). The proband of each family was presented with sensorineural hearing loss as indicated by pure-tone audiometry results. RESULTS We explored variants obtained from both families, and our analyses collectively revealed the presence and segregation of two novel loss-of-function variants: a frameshift variant, c.6347delA in MYO15A in Family I, and a splice site variant, c.5292-2A > C, in OTOF in Family II. Sanger sequencing and PCR-RFLP of DNA samples from 130 deaf and 50 control individuals confirmed that neither variant was present in our in-house database. In silico analyses predicted that each variant has a pathogenic effect on the corresponding protein. CONCLUSIONS We describe two novel loss-of-function variants in MYO15A and OTOF that cause autosomal recessive non-syndromic hearing loss in Yemeni families. Our findings are consistent with previously reported pathogenic variants in the MYO15A and OTOF genes in Middle Eastern individuals and suggest their implication in hearing loss.
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Affiliation(s)
- Maria Asaad
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE
| | - Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE
- Human Genetics and Stem Cells Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, UAE
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 - Room 107, P.O. Box 27272, Sharjah, UAE.
- Human Genetics and Stem Cells Research Group, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, UAE.
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12
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Lee YH, Tsai CY, Lu YS, Lin PH, Chiang YT, Yang TH, Hsu JSJ, Hsu CJ, Chen PL, Liu TC, Wu CC. Revisiting Genetic Epidemiology with a Refined Targeted Gene Panel for Hereditary Hearing Impairment in the Taiwanese Population. Genes (Basel) 2023; 14:genes14040880. [PMID: 37107638 PMCID: PMC10137978 DOI: 10.3390/genes14040880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Hearing impairment is one of the most common sensory disorders in children, and targeted next-generation sequencing (NGS)-based genetic examinations can assist in its prognostication and management. In 2020, we developed a simplified 30-gene NGS panel from the original 214-gene NGS version based on Taiwanese genetic epidemiology data to increase the accessibility of NGS-based examinations. In this study, we evaluated the diagnostic performance of the 30-gene NGS panel and compared it with that of the original 214-gene NGS panel in patient subgroups with different clinical features. Data on the clinical features, genetic etiologies, audiological profiles, and outcomes were collected from 350 patients who underwent NGS-based genetic examinations for idiopathic bilateral sensorineural hearing impairment between 2020 and 2022. The overall diagnostic yield was 52%, with slight differences in genetic etiology between patients with different degrees of hearing impairment and ages of onset. No significant difference was found in the diagnostic yields between the two panels, regardless of clinical features, except for a lower detection rate of the 30-gene panel in the late-onset group. For patients with negative genetic results, where the causative variant is undetectable on current NGS-based methods, part of the negative results may be due to genes not covered by the panel or yet to be identified. In such cases, the hearing prognosis varies and may decline over time, necessitating appropriate follow-up and consultation. In conclusion, genetic etiologies can serve as references for refining targeted NGS panels with satisfactory diagnostic performance.
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Affiliation(s)
- Yen-Hui Lee
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Cheng-Yu Tsai
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan
| | - Yue-Sheng Lu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Yu-Ting Chiang
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan
| | - Ting-Hua Yang
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Jacob Shu-Jui Hsu
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
- Department of Otolaryngology, Buddhist Tzuchi General Hospital, Taichung Branch, Taichung 42743, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei 10041, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
- Department of Otolaryngology, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan
- Department of Otolaryngology, National Taiwan University College of Medicine, Taipei 10002, Taiwan
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu 30261, Taiwan
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13
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Abbasi Z, Jafari Khamirani H, Tabei SMB, Manoochehri J, Dianatpour M, Dastgheib SA. EPS8 variant causes deafness, autosomal recessive 102 (DFNB102) and literature review. Hum Genome Var 2023; 10:1. [PMID: 36635257 PMCID: PMC9837036 DOI: 10.1038/s41439-023-00229-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023] Open
Abstract
Pathogenic variants in the EPS8 gene result in nonsyndromic hearing loss. This gene encodes the EPS8 protein in cochlear inner hair cells and performs critical roles in stimulating actin polymerization and bundling. Thus far, only four pathogenic variations in EPS8 have been described. In this study, we report the fifth pathogenic variant in the EPS8 gene in an Iranian patient with DFNB102. Furthermore, we review literature cases with EPS8 mutations.
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Affiliation(s)
- Zahra Abbasi
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Seyed Mohammad Bagher Tabei
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
- Maternal-fetal Medicine Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Manoochehri
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Dianatpour
- Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran
- Stem Cells Technology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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14
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Shatokhina O, Galeeva N, Stepanova A, Markova T, Lalayants M, Alekseeva N, Tavarkiladze G, Markova T, Bessonova L, Petukhova M, Guseva D, Anisimova I, Polyakov A, Ryzhkova O, Bliznetz E. Spectrum of Genes for Non- GJB2-Related Non-Syndromic Hearing Loss in the Russian Population Revealed by a Targeted Deafness Gene Panel. Int J Mol Sci 2022; 23:ijms232415748. [PMID: 36555390 PMCID: PMC9779600 DOI: 10.3390/ijms232415748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/30/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022] Open
Abstract
Hearing loss is one of the most genetically heterogeneous disorders known. Over 120 genes are reportedly associated with non-syndromic hearing loss (NSHL). To date, in Russia, there have been relatively few studies that apply massive parallel sequencing (MPS) methods to elucidate the genetic factors underlying non-GJB2-related hearing loss cases. The current study is intended to provide an understanding of the mutation spectrum in non-GJB2-related hearing loss in a cohort of Russian sensorineural NSHL patients and establish the best diagnostic algorithm. Genetic testing using an MPS panel, which included 33 NSHL and syndromic hearing loss (SHL) genes that might be misdiagnosed as NSHL genes, was completed on 226 sequentially accrued and unrelated patients. As a result, the molecular basis of deafness was found in 21% of the non-GJB2 NSHL cases. The total contribution pathogenic, and likely pathogenic, variants in the genes studied among all hereditary NSHL Russian patients was 12%. STRC pathogenic and likely pathogenic, variants accounted for 30% of diagnoses in GJB2-negative patients, providing the most common diagnosis. The majority of causative mutations in STRC involved large copy number variants (CNVs) (80%). Among the point mutations, the most common were c.11864G>A (p.Trp3955*) in the USH2A gene, c.2171_2174delTTTG (p.Val724Glyfs*6) in the STRC gene, and c.107A>C (p.His36Pro) and c.1001G>T (p.Gly334Val) in the SLC26A4 gene. Pathogenic variants in genes involved in SHL accounted for almost half of the cases with an established molecular genetic diagnosis, which were 10% of the total cohort of patients with non-GJB2-related hearing loss.
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Affiliation(s)
- Olga Shatokhina
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Nailya Galeeva
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Anna Stepanova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Tatiana Markova
- Federal State Budgetary Institution of Science “National Research Centre for Audiology and Hearing Rehabilitation”, 117513 Moscow, Russia
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education”, 125993 Moscow, Russia
| | - Maria Lalayants
- Federal State Budgetary Institution of Science “National Research Centre for Audiology and Hearing Rehabilitation”, 117513 Moscow, Russia
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education”, 125993 Moscow, Russia
| | - Natalia Alekseeva
- Federal State Budgetary Institution of Science “National Research Centre for Audiology and Hearing Rehabilitation”, 117513 Moscow, Russia
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education”, 125993 Moscow, Russia
| | - George Tavarkiladze
- Federal State Budgetary Institution of Science “National Research Centre for Audiology and Hearing Rehabilitation”, 117513 Moscow, Russia
- Federal State Budgetary Educational Institution of Further Professional Education “Russian Medical Academy of Continuous Professional Education”, 125993 Moscow, Russia
| | - Tatiana Markova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Liudmila Bessonova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Marina Petukhova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Daria Guseva
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Inga Anisimova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Alexander Polyakov
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
| | - Oxana Ryzhkova
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
- Correspondence:
| | - Elena Bliznetz
- Federal State Budgetary Institution “Research Centre For Medical Genetics”, 115478 Moscow, Russia
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15
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Yang JY, Wang WQ, Han MY, Huang SS, Wang GJ, Su Y, Xu JC, Fu Y, Kang DY, Yang K, Zhang X, Liu X, Gao X, Yuan YY, Dai P. Addition of an affected family member to a previously ascertained autosomal recessive nonsyndromic hearing loss pedigree and systematic phenotype-genotype analysis of splice-site variants in MYO15A. BMC Med Genomics 2022; 15:241. [PMCID: PMC9673454 DOI: 10.1186/s12920-022-01368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Pathogenic variants in MYO15A are known to cause autosomal recessive nonsyndromic hearing loss (ARNSHL), DFNB3. We have previously reported on one ARNSHL family including two affected siblings and identified MYO15A c.5964+3G > A and c.8375 T > C (p.Val2792Ala) as the possible deafness-causing variants. Eight year follow up identified one new affected individual in this family, who also showed congenital, severe to profound sensorineural hearing loss. By whole exome sequencing, we identified a new splice-site variant c.5531+1G > C (maternal allele), in a compound heterozygote with previously identified missense variant c.8375 T > C (p.Val2792Ala) (paternal allele) in MYO15A as the disease-causing variants. The new affected individual underwent unilateral cochlear implantation at the age of 1 year, and 5 year follow-up showed satisfactory speech and language outcomes. Our results further indicate that MYO15A-associated hearing loss is good candidates for cochlear implantation, which is in accordance with previous report. In light of our findings and review of the literatures, 58 splice-site variants in MYO15A are correlated with a severe deafness phenotype, composed of 46 canonical splice-site variants and 12 non-canonical splice-site variants.
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Affiliation(s)
- Jin-Yuan Yang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Wei-Qian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ming-Yu Han
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Sha-Sha Huang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Guo-Jian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Yu Su
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General Hospital Affiliated Hainan Hospital, Jianglin Road, Sanya, 572013 People’s Republic of China ,Hainan Province Clinical Research Center for Otolaryngologic and Head and Neck Diseases, Jianglin Road, Sanya, 572013 People’s Republic of China
| | - Jin-Cao Xu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ying Fu
- grid.27255.370000 0004 1761 1174Department of Otorhinolaryngology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Hefei Road, Qingdao, 266035 Shandong People’s Republic of China
| | - Dong-Yang Kang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Kun Yang
- grid.488137.10000 0001 2267 2324Postgraduate Training Base of Jinzhou Medical University, The PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xin Zhang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Xing Liu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xue Gao
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Yong-Yi Yuan
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Pu Dai
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
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16
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Elsayed O, Al‐Shamsi A. Mutation spectrum of non-syndromic hearing loss in the UAE, a retrospective cohort study and literature review. Mol Genet Genomic Med 2022; 10:e2052. [PMID: 36056583 PMCID: PMC9651598 DOI: 10.1002/mgg3.2052] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/23/2022] [Accepted: 08/15/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Hearing loss (HL) is a heterogeneous condition that causes partial or complete hearing impairment. Hundreds of variants in >60 genes have been reported to be associated with Hereditary HL (HHL), variants of the GJB2 gene are the most common cause of congenital SNHL, with >100 variants reported. The HHL prevalence is thought to be high in the Arab population; however, the genetic epidemiology of HHL among Emirati populations is understudied. AIMS To shed light on the mutational spectrum of NSHL in Emirati patients seen in the genetic clinic over 10 years and to capture founder mutation(s) if any were identified. METHODS Retrospective chart review of all Emirati patients assessed by clinical geneticists due to NSHL during the period between January 2010 to December 2020. Genetic tests were done based on clinical phenotypes of the patient and family history including targeted mutation testing, next-generation sequencing, or whole-exome sequencing (solo or trio). The authors did literature reviews using PubMed for all previously reported articles related to NSHL genes from UAE. RESULTS A total of 162 patients with HL, were evaluated during the period between January 2010 to December 2020. There were 82 patients with NSHL, and only 72 patients who completed the genetic evaluations were included in this retrospective study. Among the studied group, 42 (51.2%) were males and 40 (48.78%) were females. The youngest patient was 2 years old and the oldest patient was 50 years old. Consanguinity was documented in 76 patients (92.68%). A total of 14 mutations reported here are novel (23/72 i.e., 31.9%). Twelve missense mutations, 6 nonsense mutations, 6 frameshift mutations, 2 in-frame deletion mutations, and 1 splice site mutation was found. Variants in the GJB2 gene are the most commonly identified cause of NSHL, with c.35delG being the most followed by c.506G > A. The second commonly found variant is c.934C > G (p.Arg312Gly) in the CDC14A gene, found in 9 patients. This was followed by variants in OTOF and SLC26A4 genes, found in 8 patients, respectively. Chromosomal microdeletions encompassing genes causing NSHL were found in 3 patients. No mitochondrial mutations were found in this study group. A total of 11 previous reports about Emirati patients with NSHL were reviewed, with a total of 35 patients. CONCLUSION Emirati patients with NSHL have several mutations, most notably missense mutations. Novel mutations are worth further testing and represent the area for future researches.
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Affiliation(s)
- Omnia Elsayed
- Pediatrics DepartmentTawam HospitalAl AinUnited Arab Emirates
| | - Aisha Al‐Shamsi
- Genetic Division, Pediatrics DepartmentTawam HospitalAl AinUnited Arab Emirates
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17
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Kabahuma RI, Schubert W, Labuschagne C, Yan D, Pepper MS, Liu X. Elucidation of repeat motifs R1- and R2-related TRIOBP variants in autosomal recessive nonsyndromic hearing loss DFNB28 among indigenous South African individuals. Mol Genet Genomic Med 2022; 10:e2015. [PMID: 36029164 PMCID: PMC9544205 DOI: 10.1002/mgg3.2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/10/2022] [Accepted: 06/28/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND DFNB28, a recessively inherited nonsyndromic form of deafness in humans, is caused by mutations in the TRIOBP gene (MIM #609761) on chromosome 22q13. Its protein TRIOBP helps to tightly bundle F-actin filaments, forming a rootlet that penetrates through the cuticular plate into the cochlear hair cell body. Repeat motifs R1 and R2, located in exon 7 of the TRIOBP-5 isoform, are the actin-binding domains. Deletion of both repeat motifs R1 and R2 results in complete disruption of both actin-binding and bundling activities, whereas deletion of the R2 motif alone retains F-actin bundling ability in stereocilia rootlets. METHODS Target sequencing, using a custom capture panel of 180 known and candidate genes associated with sensorineural hearing loss, bioinformatics processing, and data analysis were performed. Genesis 2.0 was used for variant filtering based on quality/score read depth and minor allele frequency (MAF) thresholds of 0.005 for recessive NSHL, as reported in population-based sequencing databases. All variants were reclassified based on the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) guidelines together with other variant interpretation guidelines for genetic hearing loss . Candidate variants were confirmed via Sanger sequencing according to standard protocols, using the ABIPRISM 3730 DNA Analyzer. DNA sequence analysis was performed with DNASTAR Lasergene software. RESULTS Candidate TRIOBP variants identified among 94 indigenous sub-Saharan African individuals were characterized through segregation analysis. Family TS005 carrying variants c.572delC, p.Pro191Argfs*50, and c.3510_3513dupTGCA, p.Pro1172Cysfs*13, demonstrated perfect cosegregation with the deafness phenotype. On the other hand, variants c.505C > A p.Asp168Glu and c.3636 T > A p.Leu1212Gln in the same family did not segregate with deafness and we have classified these variants as benign. A control family, TS067, carrying variants c.2532G > T p.Leu844Arg, c.2590C > A p.Asn867Lys, c.3484C > T p.Pro1161Leu, and c.3621 T > C p.Phe1187Leu demonstrated no cosegregation allowing us to classify these variants as benign. Together with published TRIOBP variants, the results showed that genotypes combining two truncating TRIOBP variants affecting repeat motifs R1 and R2 or R2 alone lead to a deafness phenotype, while a truncating variant affecting repeat motifs R1 and R2 or R2 alone combined with a missense variant does not. Homozygous truncating variants affecting repeat motif R2 cosegregate with the deafness phenotype. CONCLUSION While a single intact R1 motif may be adequate for actin-binding and bundling in the stereocilia of cochlear hair cells, our findings indicate that a truncated R2 motif in cis seems to be incompatible with normal hearing, either by interfering with the function of an intact R1 motif or through another as yet unknown mechanism. Our study also suggests that most heterozygous missense variants involving exon 7 are likely to be tolerated.
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Affiliation(s)
- Rosemary Ida Kabahuma
- Department of OtorhinolaryngologyUniversity of PretoriaPretoriaSouth Africa,Departments of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Wolf‐Dieter Schubert
- Departments of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural SciencesUniversity of PretoriaPretoriaSouth Africa
| | | | - Denise Yan
- Department of OtolaryngologyUniversity of Miami Miller School of MedicineMiamiFloridaUSA
| | - Michael Sean Pepper
- Institute for Cellular and Molecular Medicine, Department of Immunology and SAMRC Extramural Unit for Stem Cell Research and Therapy, Faculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Xue‐Zhong Liu
- Department of OtolaryngologyUniversity of Miami Miller School of MedicineMiamiFloridaUSA
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18
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Molecular diagnose of a large hearing loss population from China by targeted genome sequencing. J Hum Genet 2022; 67:643-649. [PMID: 35982127 PMCID: PMC9592555 DOI: 10.1038/s10038-022-01066-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022]
Abstract
Hereditary hearing loss is genetically heterogeneous, with diverse clinical manifestations. Here we performed targeted genome sequencing of 227 hearing loss related genes in 1027 patients with bilateral hearing loss and 520 healthy volunteers with normal hearing to comprehensively identify the molecular etiology of hereditary hearing loss in a large cohort from China. We obtained a diagnostic rate of 57.25% (588/1027) for the patients, while 4.67% (48/1027) of the patients were identified with uncertain diagnoses. Of the implicated 35 hearing loss genes, three common genes, including SLC26A4(278/588), GJB2(207/588), MT-RNR1(19/588), accounted for 85.54% (503/588) of the diagnosed cases, while 32 uncommon hearing loss genes, including MYO15A, MITF, OTOF, POU3F4, PTPN11, etc. accounted for the remaining diagnostic rate of 14.46% (85/588). Apart from Pendred syndrome, other eight types of syndromic hearing loss were also identified. Of the 64 uncertain significant variants and 244 pathogenic/likely pathogenic variants identified in the patients, 129 novel variants were also detected. Thus, the molecular etiology presented with high heterogeneity with the leading causes to be SLC26A4 and GJB2 genes in the Chinese hearing loss population. It’s urgent to develop a database of the ethnicity-matched healthy population as well as to perform functional studies for further classification of uncertain significant variants.
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19
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Ju D, Hui D, Hammond DA, Wonkam A, Tishkoff SA. Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine. Annu Rev Biomed Data Sci 2022; 5:321-339. [PMID: 35576557 PMCID: PMC9904154 DOI: 10.1146/annurev-biodatasci-122220-112550] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
One goal of genomic medicine is to uncover an individual's genetic risk for disease, which generally requires data connecting genotype to phenotype, as done in genome-wide association studies (GWAS). While there may be clinical promise to employing prediction tools such as polygenic risk scores (PRS), it currently stands that individuals of non-European ancestry may not reap the benefits of genomic medicine because of underrepresentation in large-scale genetics studies. Here, we discuss why this inequity poses a problem for genomic medicine and the reasons for the low transferability of PRS across populations. We also survey the ancestry representation of published GWAS and investigate how estimates of ancestry diversity in GWASparticipants might be biased. We highlight the importance of expanding genetic research in Africa, one of the most underrepresented regions in human genomics research, and discuss issues of ethics, resources, and technology for equitable advancement of genomic medicine.
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Affiliation(s)
- Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Daniel Hui
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Graduate Program in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dorothy A Hammond
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Penn Center for Global Genomics & Health Equity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA;
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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20
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Childhood Hearing Health and Early Language Exposure: A Culturally Sensitive Approach. Adv Pediatr 2022; 69:23-39. [PMID: 35985712 DOI: 10.1016/j.yapd.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Implementation of the universal newborn hearing screening has changed the landscape for children born deaf or hard of hearing, and with this, pediatricians must be knowledgeable about the screening and referral process, state protocols, and how to support patients and their families in their unique journeys. Early access to language-spoken, signed, both-forms the foundation for successful outcomes for the development of fluent language. For children using spoken language, early access to sound is critical and can often be achieved with the assistance of hearing devices, even in the newborn period. For all language modalities, state-funded Deaf mentor programs allow families to have meaningful exposure to the Deaf community. The authors come from different professions in the health care and education fields, including General Pediatrics, Otolaryngology Head and Neck Surgery, and the state Department of Education, and use different languages, including spoken and American Sign Language.
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21
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Imtiaz A. ARNSHL gene identification: past, present and future. Mol Genet Genomics 2022; 297:1185-1193. [DOI: 10.1007/s00438-022-01926-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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22
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Mutations in MINAR2 encoding membrane integral NOTCH2-associated receptor 2 cause deafness in humans and mice. Proc Natl Acad Sci U S A 2022; 119:e2204084119. [PMID: 35727972 PMCID: PMC9245706 DOI: 10.1073/pnas.2204084119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Discovery of deafness genes and elucidating their functions have substantially contributed to our understanding of hearing physiology and its pathologies. Here we report on DNA variants in MINAR2, encoding membrane integral NOTCH2-associated receptor 2, in four families underlying autosomal recessive nonsyndromic deafness. Neurologic evaluation of affected individuals at ages ranging from 4 to 80 y old does not show additional abnormalities. MINAR2 is a recently annotated gene with limited functional understanding. We detected three MINAR2 variants, c.144G > A (p.Trp48*), c.412_419delCGGTTTTG (p.Arg138Valfs*10), and c.393G > T, in 13 individuals with congenital- or prelingual-onset severe-to-profound sensorineural hearing loss (HL). The c.393G > T variant is shown to disrupt a splice donor site. We show that Minar2 is expressed in the mouse inner ear, with the protein localizing mainly in the hair cells, spiral ganglia, the spiral limbus, and the stria vascularis. Mice with loss of function of the Minar2 protein (Minar2tm1b/tm1b) present with rapidly progressive sensorineural HL associated with a reduction in outer hair cell stereocilia in the shortest row and degeneration of hair cells at a later age. We conclude that MINAR2 is essential for hearing in humans and mice and its disruption leads to sensorineural HL. Progressive HL observed in mice and in some affected individuals and as well as relative preservation of hair cells provides an opportunity to interfere with HL using genetic therapies.
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23
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Wonkam A, Adadey SM, Schrauwen I, Aboagye ET, Wonkam-Tingang E, Esoh K, Popel K, Manyisa N, Jonas M, deKock C, Nembaware V, Cornejo Sanchez DM, Bharadwaj T, Nasir A, Everard JL, Kadlubowska MK, Nouel-Saied LM, Acharya A, Quaye O, Amedofu GK, Awandare GA, Leal SM. Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes. Commun Biol 2022; 5:369. [PMID: 35440622 PMCID: PMC9019055 DOI: 10.1038/s42003-022-03326-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/25/2022] [Indexed: 12/15/2022] Open
Abstract
We investigated hearing impairment (HI) in 51 families from Ghana with at least two affected members that were negative for GJB2 pathogenic variants. DNA samples from 184 family members underwent whole-exome sequencing (WES). Variants were found in 14 known non-syndromic HI (NSHI) genes [26/51 (51.0%) families], five genes that can underlie either syndromic HI or NSHI [13/51 (25.5%)], and one syndromic HI gene [1/51 (2.0%)]. Variants in CDH23 and MYO15A contributed the most to HI [31.4% (16/51 families)]. For DSPP, an autosomal recessive mode of inheritance was detected. Post-lingual expression was observed for a family segregating a MARVELD2 variant. To our knowledge, seven novel candidate HI genes were identified (13.7%), with six associated with NSHI (INPP4B, CCDC141, MYO19, DNAH11, POTEI, and SOX9); and one (PAX8) with Waardenburg syndrome. MYO19 and DNAH11 were replicated in unrelated Ghanaian probands. Six of the novel genes were expressed in mouse inner ear. It is known that Pax8-/- mice do not respond to sound, and depletion of Sox9 resulted in defective vestibular structures and abnormal utricle development. Most variants (48/60; 80.0%) have not previously been associated with HI. Identifying seven candidate genes in this study emphasizes the potential of novel HI genes discovery in Africa.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Elvis Twumasi Aboagye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Kalinka Popel
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Mario Jonas
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Carmen deKock
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
| | - Diana M Cornejo Sanchez
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon-si, Republic of Korea
| | - Jenna L Everard
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Magda K Kadlubowska
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Geoffrey K Amedofu
- Department of Eye, Ear, Nose, and Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, LG 54, Ghana
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Centre, New York, NY, 10032, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Centre, New York, NY, 10032, USA.
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24
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Domínguez-Ruiz M, Rodríguez-Ballesteros M, Gandía M, Gómez-Rosas E, Villamar M, Scimemi P, Mancini P, Rendtorff ND, Moreno-Pelayo MA, Tranebjaerg L, Medà C, Santarelli R, del Castillo I. Novel Pathogenic Variants in PJVK, the Gene Encoding Pejvakin, in Subjects with Autosomal Recessive Non-Syndromic Hearing Impairment and Auditory Neuropathy Spectrum Disorder. Genes (Basel) 2022; 13:149. [PMID: 35052489 PMCID: PMC8775161 DOI: 10.3390/genes13010149] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 01/27/2023] Open
Abstract
Pathogenic variants in the PJVK gene cause the DFNB59 type of autosomal recessive non-syndromic hearing impairment (AR-NSHI). Phenotypes are not homogeneous, as a few subjects show auditory neuropathy spectrum disorder (ANSD), while others show cochlear hearing loss. The numbers of reported cases and pathogenic variants are still small to establish accurate genotype-phenotype correlations. We investigated a cohort of 77 Spanish familial cases of AR-NSHI, in whom DFNB1 had been excluded, and a cohort of 84 simplex cases with isolated ANSD in whom OTOF variants had been excluded. All seven exons and exon-intron boundaries of the PJVK gene were sequenced. We report three novel DFNB59 cases, one from the AR-NSHI cohort and two from the ANSD cohort, with stable, severe to profound NSHI. Two of the subjects received unilateral cochlear implantation, with apparent good outcomes. Our study expands the spectrum of PJVK mutations, as we report four novel pathogenic variants: p.Leu224Arg, p.His294Ilefs*43, p.His294Asp and p.Phe317Serfs*20. We review the reported cases of DFNB59, summarize the clinical features of this rare subtype of AR-NSHI and discuss the involvement of PJVK in ANSD.
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Affiliation(s)
- María Domínguez-Ruiz
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Montserrat Rodríguez-Ballesteros
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Marta Gandía
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Elena Gómez-Rosas
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Manuela Villamar
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Pietro Scimemi
- Department of Neurosciences, University of Padua, 35121 Padua, Italy; (P.S.); (R.S.)
- Audiology Service, Santi Giovanni e Paolo Hospital, 30122 Venice, Italy
| | - Patrizia Mancini
- Department of Sense Organs, University La Sapienza, 00162 Rome, Italy;
| | - Nanna D. Rendtorff
- Department of Clinical Genetics, University Hospital, Copenhagen/The Kennedy Centre, DK-2600 Glostrup, Denmark; (N.D.R.); (L.T.)
| | - Miguel A. Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
| | - Lisbeth Tranebjaerg
- Department of Clinical Genetics, University Hospital, Copenhagen/The Kennedy Centre, DK-2600 Glostrup, Denmark; (N.D.R.); (L.T.)
- Department of Clinical Medicine, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Carme Medà
- Unidad de Prevención de Enfermedades del Oído, Conselleria de Salut, Illes Balears, 07120 Palma de Mallorca, Spain;
| | - Rosamaria Santarelli
- Department of Neurosciences, University of Padua, 35121 Padua, Italy; (P.S.); (R.S.)
- Audiology Service, Santi Giovanni e Paolo Hospital, 30122 Venice, Italy
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS, 28034 Madrid, Spain; (M.D.-R.); (M.R.-B.); (M.G.); (E.G.-R.); (M.V.); (M.A.M.-P.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 28034 Madrid, Spain
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25
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Said MB, Ayed IB, Elloumi I, Hasnaoui M, Souissi A, Idriss N, Aloulou H, Chabchoub I, Maâlej B, Driss D, Masmoudi S. Custom Next-Generation Sequencing Identifies Novel Mutations Expanding the Molecular and clinical spectrum of isolated Hearing Impairment or along with defects of the retina, the thyroid, and the kidneys. Mol Genet Genomic Med 2022; 10:e1868. [PMID: 34997822 PMCID: PMC8830811 DOI: 10.1002/mgg3.1868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/16/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022] Open
Abstract
Background In the Tunisian population, the molecular analysis of hearing impairment remains based on conventional approaches, which makes the task laborious and enormously expensive. Exploration of the etiology of Hearing Impairment and the early diagnosis of causal mutations by next‐generation sequencing help significantly alleviate social and economic problems. Methods We elaborated a custom SureSelectQXT panel for next‐generation sequencing of the coding sequences of 42 genes involved in isolated hearing impairment or along with defects of the retina, the thyroid, and the kidneys. Results We report eight pathogenic variants, four of which are novel in patients with isolated hearing impairment, hearing impairment, and renal tubular acidosis, Usher syndrome and Pendred syndrome. Functional studies using molecular modeling showed the severe impact of the novel missense mutations on the concerned proteins. Basically, we identified mutations in nuclear as well as mitochondrial genes in a Tunisian family with isolated hearing impairment, which explains definitely the phenotype detected since 2006. Conclusion Our results expanded the mutation spectrum and genotype‒phenotype correlation of isolated and syndromic hearing loss and also emphasized the importance of combining both targeted next‐generation sequencing and detailed clinical evaluation to elaborate a more accurate diagnosis for hearing impairment and related phenotypes especially in North African populations.
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Affiliation(s)
- Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetics Department, Hedi Chaker University Hospital of Sfax, Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Mehdi Hasnaoui
- Department of Otorhinolaryngology, Tahar Sfar University Hospital of Mahdia, Sfax, Tunisia
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nabil Idriss
- Department of Otorhinolaryngology, Tahar Sfar University Hospital of Mahdia, Sfax, Tunisia
| | - Hajer Aloulou
- Pediatric Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Imen Chabchoub
- Pediatric Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Bayen Maâlej
- Pediatric Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Dorra Driss
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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26
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Confirmation of COL4A6 variants in X-linked nonsyndromic hearing loss and its clinical implications. Eur J Hum Genet 2022; 30:7-12. [PMID: 33840813 PMCID: PMC8738723 DOI: 10.1038/s41431-021-00881-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/18/2021] [Accepted: 03/25/2021] [Indexed: 01/03/2023] Open
Abstract
Hearing loss (HL) is one of the most common sensory defects, of which X-linked nonsyndromic hearing loss (NSHL) accounts for only 1-2%. While a COL4A6 variant has been reported in a single Hungarian family with NSHL associated with inner ear malformation, causative role of COL4A6 variants and their phenotypic consequences in NSHL remain elusive. Here we report two families in which we identified a male member with X-linked HL. Each has inherited a rare hemizygous COL4A6 variant from their respective mothers, NM_001287758.1: c.3272 G > C (p.Gly1091Ala) and c.951 + 1 G > C. An in vitro minigene splicing assay revealed that c.951 + 1 G > T leads to skipping of exon 15, strongly suggesting a pathogenic role for this variant in the HL phenotype. The p.Gly1091Ala variant is classified as a variant of unknown significance based on the variant interpretation guidelines. This report provides evidence for variants in the COL4A6 gene resulting in X-linked NSHL. It highlights the importance of in-depth genetic studies in all family members in addition to the proband, especially in multiplex families, to determine the precise etiology of HL.
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27
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Ray M, Sarkar S, Sable MN. Genetics Landscape of Nonsyndromic Hearing Loss in Indian Populations. J Pediatr Genet 2021; 11:5-14. [PMID: 35186384 PMCID: PMC8847051 DOI: 10.1055/s-0041-1740532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 12/16/2022]
Abstract
Congenital nonsyndromic hearing loss (NSHL) has been considered as one of the most prevalent chronic disorder in children. It affects the physical and mental conditions of a large children population worldwide. Because of the genetic heterogeneity, the identification of target gene is very challenging. However, gap junction β-2 ( GJB2 ) is taken as the key gene for hearing loss, as its involvement has been reported frequently in NSHL cases. This study aimed to identify the association of GJB2 mutants in different Indian populations based on published studies in Indian population. This will provide clear genetic fundamental of NSHL in Indian biogeography, which would be helpful in the diagnosis process.
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Affiliation(s)
- Manisha Ray
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Saurav Sarkar
- Department of Otolaryngology, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India
| | - Mukund Namdev Sable
- Department of Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhubaneswar, Odisha, India,Address for correspondence Mukund Namdev Sable, MD Department of Pathology and Lab Medicine, All India Institute of Medical SciencesBhubaneswar 751019, OdishaIndia
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28
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Zhou C, Xiao Y, Xie H, Wang J, Liu S. Case Report: Novel Compound Heterozygous Variants in TRIOBP Associated With Congenital Deafness in a Chinese Family. Front Genet 2021; 12:766973. [PMID: 34868251 PMCID: PMC8635749 DOI: 10.3389/fgene.2021.766973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Autosomal recessive non-syndromic deafness-28 (DFNB28) is characterized by prelingual, profound sensorineural hearing loss (HL). The disease is related to variants of the TRIOBP gene. TRIO and F-actin binding protein (TRIOBP) plays crucial roles in modulating the assembly of the actin cytoskeleton and are responsible for the proper structure and function of stereocilia in the inner ear. This study aimed to identify pathogenic variants in a patient with HL. Genomic DNA obtained from a 33-year-old woman with HL was evaluated using a disease-targeted gene panel. Using next generation sequencing and bioinformatics analysis, we identified two novel TRIOBP c.1170delC (p.S391Pfs*488) and c.3764C > G (p.S1255*) variants. Both parents of the patient were heterozygous carriers of the gene. The two variants have not been reported in general population databases or published literature. The findings of this study will broaden the spectrum of pathogenic variants in the TRIOBP gene.
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Affiliation(s)
- Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuanyuan Xiao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hanbing Xie
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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29
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Liu W, Johansson Å, Rask-Andersen H, Rask-Andersen M. A combined genome-wide association and molecular study of age-related hearing loss in H. sapiens. BMC Med 2021; 19:302. [PMID: 34847940 PMCID: PMC8638543 DOI: 10.1186/s12916-021-02169-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Sensorineural hearing loss is one of the most common sensory deficiencies. However, the molecular contribution to age-related hearing loss is not fully elucidated. METHODS We performed genome-wide association studies (GWAS) for hearing loss-related traits in the UK Biobank (N = 362,396) and selected a high confidence set of ten hearing-associated gene products for staining in human cochlear samples: EYA4, LMX1A, PTK2/FAK, UBE3B, MMP2, SYNJ2, GRM5, TRIOBP, LMO-7, and NOX4. RESULTS All proteins were found to be expressed in human cochlear structures. Our findings illustrate cochlear structures that mediate mechano-electric transduction of auditory stimuli, neuronal conductance, and neuronal plasticity to be involved in age-related hearing loss. CONCLUSIONS Our results suggest common genetic variation to influence structural resilience to damage as well as cochlear recovery after trauma, which protect against accumulated damage to cochlear structures and the development of hearing loss over time.
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Affiliation(s)
- Wei Liu
- Department of Surgical Sciences, Section of Otorhinolaryngology and Head & Neck Surgery, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helge Rask-Andersen
- Department of Surgical Sciences, Section of Otorhinolaryngology and Head & Neck Surgery, Uppsala University, SE-751 85, Uppsala, Sweden.
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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30
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Adeyemo A, Faridi R, Chattaraj P, Yousaf R, Tona R, Okorie S, Bharadwaj T, Nouel-Saied LM, Acharya A, Schrauwen I, Morell RJ, Leal SM, Friedman TB, Griffith AJ, Roux I. Genomic analysis of childhood hearing loss in the Yoruba population of Nigeria. Eur J Hum Genet 2021; 30:42-52. [PMID: 34837038 PMCID: PMC8738750 DOI: 10.1038/s41431-021-00984-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/02/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Although variant alleles of hundreds of genes are associated with sensorineural deafness in children, the genes and alleles involved remain largely unknown in the Sub-Saharan regions of Africa. We ascertained 56 small families mainly of Yoruba ethno-lingual ancestry in or near Ibadan, Nigeria, that had at least one individual with nonsyndromic, severe-to-profound, prelingual-onset, bilateral hearing loss not attributed to nongenetic factors. We performed a combination of exome and Sanger sequencing analyses to evaluate both nuclear and mitochondrial genomes. No biallelic pathogenic variants were identified in GJB2, a common cause of deafness in many populations. Potential causative variants were identified in genes associated with nonsyndromic hearing loss (CIB2, COL11A1, ILDR1, MYO15A, TMPRSS3, and WFS1), nonsyndromic hearing loss or Usher syndrome (CDH23, MYO7A, PCDH15, and USH2A), and other syndromic forms of hearing loss (CHD7, OPA1, and SPTLC1). Several rare mitochondrial variants, including m.1555A>G, were detected in the gene MT-RNR1 but not in control Yoruba samples. Overall, 20 (33%) of 60 independent cases of hearing loss in this cohort of families were associated with likely causal variants in genes reported to underlie deafness in other populations. None of these likely causal variants were present in more than one family, most were detected as compound heterozygotes, and 77% had not been previously associated with hearing loss. These results indicate an unusually high level of genetic heterogeneity of hearing loss in Ibadan, Nigeria and point to challenges for molecular genetic screening, counseling, and early intervention in this population.
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Affiliation(s)
- Adebolajo Adeyemo
- Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Parna Chattaraj
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Okorie
- Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Robert J Morell
- Genomics and Computational Biology Core, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, 630 W 168th St, New York, NY, 10032, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew J Griffith
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Otolaryngology, College of Medicine, University of Tennessee Health Science Center, 910 Madison Avenue, Memphis, TN, 38163, USA
| | - Isabelle Roux
- Otolaryngology Branch, NIDCD, National Institutes of Health, Bethesda, MD, 20892, USA.
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31
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Yu S, Chen WX, Zhang YF, Ni Y, Lu P, Wang B, Wang Y, Wu B, Ni Q, Wang H, Xu ZM. Apparent homozygosity for a novel splicing variant in EPS8 causes congenital profound hearing loss. Eur J Med Genet 2021; 64:104362. [PMID: 34637946 DOI: 10.1016/j.ejmg.2021.104362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/17/2021] [Accepted: 10/08/2021] [Indexed: 12/27/2022]
Abstract
Autosomal recessive deafness-102 (DFNB102), a new profound prelingual non-syndromic hearing loss, is caused by mutations in the EPS8 gene. To date, only three such consanguineous families with three different homozygous variants in EPS8 have been reported. Here, we report the fourth case from a non-consanguineous Chinese family, an 11-month-old male infant presented with congenital profound non-syndromic hearing loss. Trio whole-exome sequencing initially identified the patient with a novel seemingly homozygous splicing variant NM_004447.5: c.1435-2A > T in intron 14 of the EPS8 gene and was inherited from his father; further CNVs analysis identified a novel 65.9 kb intragenic deletion and was inherited from his mother. The deletion is covering intron 14 that could account for the apparent homozygosity of the patient. In vitro splicing assay showed the variant c.1435-2A > T creates a new donor site at position c.1443, which is predicted to produce a stop codon after 14 additional amino acids (p.His479Cysfs*14). Furthermore, quantitative allele-specific expression assay showed that relative EPS8 gene expression in the patient significantly decreased (0-fold for the wild-type transcript and 0.25-0.27-fold for the mutant transcript) compared to the control (P < 0.05), indicating the pathogenicity of the identified variants. Overall, our study provides additional evidence that EPS8 is a causative gene for DFNB102 and highlights the clinical utility of simultaneous analysis of CNVs and SNVs to avoid potential errors in the diagnosis and interpretation of patients with apparent homozygosity.
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Affiliation(s)
- Sha Yu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wen-Xia Chen
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun-Fei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yihua Ni
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Lu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bin Wang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yan Wang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Zheng-Min Xu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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32
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Adadey SM, Wonkam-Tingang E, Aboagye ET, Quaye O, Awandare GA, Wonkam A. Hearing loss in Africa: current genetic profile. Hum Genet 2021; 141:505-517. [PMID: 34609590 PMCID: PMC9034983 DOI: 10.1007/s00439-021-02376-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023]
Abstract
Hearing impairment (HI) is highly heterogeneous with over 123 associated genes reported to date, mostly from studies among Europeans and Asians. Here, we performed a systematic review of literature on the genetic profile of HI in Africa. The study protocol was registered on PROSPERO, International Prospective Register of Systematic Reviews with the registration number “CRD42021240852”. Literature search was conducted on PubMed, Scopus, Africa-Wide Information, and Web of Science databases. A total of 89 full-text records was selected and retrieved for data extraction and analyses. We found reports from only 17/54 (31.5%) African countries. The majority (61/89; 68.5%) of articles were from North Africa, with few reports found from sub-Saharan Africa. The most common method used in these publications was targeted gene sequencing (n = 66/111; 59.5%), and only 13.5% (n = 15/111) used whole-exome sequencing. More than half of the studies were performed in families segregating HI (n = 51/89). GJB2 was the most investigated gene, with GJB2: p.(R143W) founder variant only reported in Ghana, while GJB2: c.35delG was common in North African countries. Variants in MYO15A were the second frequently reported in both North and Central Africa, followed by ATP6V1B1 only reported from North Africa. Usher syndrome was the main syndromic HI molecularly investigated, with variants in five genes reported: USH2A, USH1G, USH1C, MYO7A, and PCDH15. MYO7A: p.(P1780S) founder variant was reported as the common Usher syndrome variant among Black South Africans. This review provides the most comprehensive data on HI gene variants in the largely under-investigated African populations. Future exomes studies particularly in multiplex families will likely provide opportunities for the discovery of the next sets of novel HI genes, and well as unreported variants in known genes to further our understanding of HI pathobiology, globally.
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Affiliation(s)
- Samuel Mawuli Adadey
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana.,Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa
| | - Elvis Twumasi Aboagye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Gordon A Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, P.O. Box LG 54, Legon, Accra, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.
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Usami SI, Nishio SY. The genetic etiology of hearing loss in Japan revealed by the social health insurance-based genetic testing of 10K patients. Hum Genet 2021; 141:665-681. [PMID: 34599366 PMCID: PMC9035015 DOI: 10.1007/s00439-021-02371-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
Etiological studies have shown genetic disorders to be a major cause of sensorineural hearing loss, but there are a limited number of comprehensive etiological reports based on genetic analysis. In the present study, the same platform using a diagnostic DNA panel carrying 63 deafness genes and the same filtering algorithm were applied to 10,047 samples obtained from social health insurance-based genetic testing of hearing loss. The most remarkable result obtained in this comprehensive study was that the data first clarified the genetic epidemiology from congenital/early-onset deafness to late-onset hearing loss. The overall diagnostic rate was 38.8%, with the rate differing for each age group; 48.6% for the congenital/early-onset group (~5y.o.), 33.5% for the juvenile/young adult-onset group, and 18.0% for the 40+ y.o. group. Interestingly, each group showed a different kind of causative gene. With regard to the mutational spectra, there are certain recurrent variants that may be due to founder effects or hot spots. A series of haplotype studies have shown many recurrent variants are due to founder effects, which is compatible with human migration. It should be noted that, regardless of differences in the mutational spectrum, the clinical characteristics caused by particular genes can be considered universal. This comprehensive review clarified the detailed clinical characteristics (onset age, severity, progressiveness, etc.) of hearing loss caused by each gene, and will provide useful information for future clinical application, including genetic counseling and selection of appropriate interventions.
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Affiliation(s)
- Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan.
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Japan
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34
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Florentine MM, Rouse SL, Stephans J, Conrad D, Czechowicz J, Matthews IR, Meyer AK, Nadaraja GS, Parikh R, Virbalas J, Weinstein JE, Chan DK. Racial and ethnic disparities in diagnostic efficacy of comprehensive genetic testing for sensorineural hearing loss. Hum Genet 2021; 141:495-504. [PMID: 34515852 PMCID: PMC9035005 DOI: 10.1007/s00439-021-02338-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022]
Abstract
Understanding racial and ethnic disparities in diagnostic rates of genetic testing is critical for health equity. We sought to understand the extent and cause of racial and ethnic disparities in diagnostic efficacy of comprehensive genetic testing (CGT) for sensorineural hearing loss (SNHL). We performed a retrospective cohort study at two tertiary children’s hospitals on a diverse cohort of 240 consecutive pediatric patients (76% publicly insured, 82% non-White) with SNHL of unknown etiology who underwent CGT. Definite and possible genetic diagnoses were assigned for each patient, representing the likelihood of a genetic cause of hearing loss. Associations between diagnostic rates were examined. 3.8 ± 2.1 variants were detected per patient; this frequency did not vary between White/Asian and Hispanic/Black cohorts. Overall, 82% of variants were variants of uncertain significance (VUS). Compared with White and Asian subjects, variants identified among Hispanic and Black children were less likely to be classified as pathogenic/likely pathogenic (15% vs. 24%, p < 0.001), and Hispanic and Black children were less likely to have a definite genetic diagnosis (10% vs. 37%, p < 0.001). The adjusted odds ratio for definite genetic diagnosis in Black and Hispanic children compared with White and Asian children was 0.19. Expanding genetic diagnostic criteria to include predicted deleterious VUSs reduced these disparities between White/Asian and Hispanic/Black children, with comparable molecular diagnostic rates (41% vs. 38%, p = 0.72). However, in silico predictions are insufficiently valid for clinical use. Increased inclusion of underrepresented groups in genetic hearing-loss studies to clinically validate these variants is necessary to reduce racial and ethnic disparities in diagnostic efficacy of comprehensive genetic testing.
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Affiliation(s)
- Michelle M Florentine
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Stephanie L Rouse
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Jihyun Stephans
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - David Conrad
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Josephine Czechowicz
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Ian R Matthews
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Anna K Meyer
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Garani S Nadaraja
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Rajan Parikh
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Jordan Virbalas
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Jacqueline E Weinstein
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Dylan K Chan
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA. .,Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.
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Rouse SL, Florentine MM, Taketa E, Chan DK. Racial and ethnic disparities in genetic testing for hearing loss: a systematic review and synthesis. Hum Genet 2021; 141:485-494. [PMID: 34494120 PMCID: PMC9035011 DOI: 10.1007/s00439-021-02335-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 11/26/2022]
Abstract
Racial/ethnic disparities in the diagnostic efficacy of genetic testing for hearing loss have been described. These disparities may relate to differences in variant classification between different racial/ethnic groups, which may, in turn, derive from disparate representation of these groups in the published literature. We sought to quantify racial/ethnic disparities in the published literature on the human genetics of hearing loss. We conducted a search of PubMed for articles describing single-gene, multiple-gene, or whole-exome sequencing for individuals with sensorineural hearing loss. Data on the included subjects, including race/ethnicity and/or region of origin, a number of subjects tested, and method of testing, were extracted. 1355 populations representing 311,092 subjects from 1165 studies were included. Overall, subjects of European and Asian ancestry were equivalently represented, but those of Latino American, African, and indigenous North American ancestry were significantly underrepresented; over 96% of all subjects in the published literature were European or Asian. Within populations, the majority of subjects derived from a small subset of countries. The observed disparity was greater for multiple-gene and whole-exome sequencing than for single-gene sequencing. These findings illustrate the large disparity in the published literature on the genetics of hearing loss, and demonstrate the need for increased representation of Latino American, African, and indigenous North American populations.
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Affiliation(s)
| | - Michelle M Florentine
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Emily Taketa
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA
| | - Dylan K Chan
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.
- Division of Pediatric Otolaryngology-Head and Neck Surgery, University of California-San Francisco, 2233 Post Street, Third Floor, San Francisco, CA, 94115, USA.
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Guan J, Li J, Chen G, Shi T, Lan L, Wu X, Zhao C, Wang D, Wang H, Wang Q. Family trio-based sequencing in 404 sporadic bilateral hearing loss patients discovers recessive and De novo genetic variants in multiple ways. Eur J Med Genet 2021; 64:104311. [PMID: 34416374 DOI: 10.1016/j.ejmg.2021.104311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 08/07/2021] [Accepted: 08/15/2021] [Indexed: 11/29/2022]
Abstract
Hereditary hearing loss (HL) has high genetic and phenotypical heterogeneity including the overlapping and variable phenotypic features. For sporadic HL without a family history, it is more difficult to indicate the contribution of genetic factors to define a pattern of inheritance. We assessed the contribution of genetic variants and patterns of inheritance by a family trio-based sequencing and provided new insight into genetics. We conducted an analysis of data from unrelated sporadic patients with HL (n = 404) who underwent trio-based whole-exome sequencing (trio-WES) or proband-only WES (p-WES) or targeted exome sequencing (TES), and the samples of their unaffected-parents (n = 808)were validated. A molecular diagnosis was rendered for 191 of 404 sporadic HL patients (47.3%) in multiple modes of inheritance, including autosomal recessive (AR), autosomal dominant (AD) caused by de novo variants, copy-number variants (CNVs), X-linked recessive, and dual genetic diagnosis. Among these patients, 83 (43.5%) cases were diagnosed with variants in rare genes. Sporadic HL patients were identified by multiple modes of transmission. Observed variations in rare genes and multiple modes of inheritance can strikingly emphasize the important etiological contribution of recessive and de novo genetic variants to a large cohort of sporadic HL cases plus their parents.
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Affiliation(s)
- Jing Guan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Jin Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Guohui Chen
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Tao Shi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Lan Lan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Xiaonan Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Cui Zhao
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Dayong Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Hongyang Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Qiuju Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
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Nasrniya S, Miar P, Narrei S, Sepehrnejad M, Nilforoush MH, Abtahi H, Tabatabaiefar MA. Whole-Exome Sequencing Identifies a Recurrent Small In-Frame Deletion in MYO15A Causing Autosomal Recessive Nonsyndromic Hearing Loss in 3 Iranian Pedigrees. Lab Med 2021; 53:111-122. [PMID: 34388253 DOI: 10.1093/labmed/lmab047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Hearing loss (HL) is the most prevalent and genetically heterogeneous sensory disabilities in humans throughout the world. METHODS In this study, we used whole-exome sequencing (WES) to determine the variant causing autosomal recessive nonsyndromic hearing loss (ARNSHL) segregating in 3 separate Iranian consanguineous families (with 3 different ethnicities: Azeri, Persian, and Lur), followed by cosegregation analysis, computational analysis, and structural modeling using the I-TASSER (Iterative Threading ASSEmbly Refinement) server. Also, we used speech-perception tests to measure cochlear implant (CI) performance in patients. RESULTS One small in-frame deletion variant (MYO15A c.8309_8311del (p.Glu2770del)), resulting in deletion of a single amino-acid residue was identified. We found it to be cosegregating with the disease in the studied families. We provide some evidence suggesting the pathogenesis of this variant in HL based on the American College of Medical Genetics (ACMG) and Genomics guidelines. Evaluation of auditory and speech performance indicated favorable outcome after cochlear implantation in our patients. CONCLUSIONS The findings of this study demonstrate the utility of WES in genetic diagnostics of HL.
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Affiliation(s)
- Samane Nasrniya
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Paniz Miar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sina Narrei
- Erythron Pathobiology and Genetics lab, Isfahan, Iran
| | - Mahsa Sepehrnejad
- Department of Audiology, School of Rehabilitation Sciences, Isfahan University of Medical Sciences University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hussein Nilforoush
- Department of Audiology, School of Rehabilitation Sciences, Isfahan University of Medical Sciences University of Medical Sciences, Isfahan, Iran
| | - Hamidreza Abtahi
- Department of Otolaryngology, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.,Department of Ear, Nose & Throat, and Head & Neck Surgery, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Erythron Pathobiology and Genetics lab, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
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Vanniya S P, Chandru J, Jeffrey JM, Rabinowitz T, Brownstein Z, Krishnamoorthy M, Avraham KB, Cheng L, Shomron N, Srisailapathy CRS. PNPT1, MYO15A, PTPRQ, and SLC12A2-associated genetic and phenotypic heterogeneity among hearing impaired assortative mating families in Southern India. Ann Hum Genet 2021; 86:1-13. [PMID: 34374074 DOI: 10.1111/ahg.12442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022]
Abstract
The study was conducted between 2018 and 2020. From a cohort of 113 hearing impaired (HI), five non-DFNB12 probands identified with heterozygous CDH23 variants were subjected to exome analysis. This resolved the etiology of hearing loss (HL) in four South Indian assortative mating families. Six variants, including three novel ones, were identified in four genes: PNPT1 p.(Ala46Gly) and p.(Asn540Ser), MYO15A p.(Leu1485Pro) and p.(Tyr1891Ter), PTPRQ p.(Gln1336Ter), and SLC12A2 p.(Pro988Ser). Compound heterozygous PNPT1 variants were associated with DFNB70 causing prelingual profound sensorineural hearing loss (SNHL), vestibular dysfunction, and unilateral progressive vision loss in one family. In the second family, MYO15A variants in the myosin motor domain, including a novel variant, causing DFNB3, were found to be associated with prelingual profound SNHL. A novel PTPRQ variant was associated with postlingual progressive sensorineural/mixed HL and vestibular dysfunction in the third family with DFNB84A. In the fourth family, the SLC12A2 novel variant was found to segregate with severe-to-profound HL causing DFNA78, across three generations. Our results suggest a high level of allelic, genotypic, and phenotypic heterogeneity of HL in these families. This study is the first to report the association of PNPT1, PTPRQ, and SLC12A2 variants with HL in the Indian population.
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Affiliation(s)
- Paridhy Vanniya S
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Jayasankaran Chandru
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India.,LifeBytes India Pvt. Ltd., Bengaluru, India
| | - Justin Margret Jeffrey
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Tom Rabinowitz
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zippora Brownstein
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Mathuravalli Krishnamoorthy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Le Cheng
- BGI Genomics, Shenzhen, P. R. China
| | - Noam Shomron
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - C R Srikumari Srisailapathy
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Chennai, India
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Frohne A, Koenighofer M, Liu DT, Laccone F, Neesen J, Gstoettner W, Schoefer C, Lucas T, Frei K, Parzefall T. High Prevalence of MYO6 Variants in an Austrian Patient Cohort With Autosomal Dominant Hereditary Hearing Loss. Otol Neurotol 2021; 42:e648-e657. [PMID: 33710140 DOI: 10.1097/mao.0000000000003076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Genetic hearing loss (HL) is often monogenic. Whereas more than half of autosomal recessive (AR) cases in Austria are caused by mutations in a single gene, no disproportionately frequent contributing genetic factor has been identified in cases of autosomal dominant (AD) HL. The genetic characterization of HL continues to improve diagnosis, genetic counseling, and lays a foundation for the development of personalized medicine approaches. METHODS Diagnostic HL panel screening was performed in an Austrian multiplex family with AD HL, and segregation was tested with polymerase chain reaction and Sanger sequencing. In an independent approach, 18 unrelated patients with AD HL were screened for causative variants in all known HL genes to date and segregation was tested if additional family members were available. The pathogenicity of novel variants was assessed based on previous literature and bioinformatic tools such as prediction software and protein modeling. RESULTS In six of the 19 families under study, candidate pathogenic variants were identified in MYO6, including three novel variants (p.Gln441Pro, p.Ser612Tyr, and p.Gln650ValfsTer7). Some patients carried more than one likely pathogenic variant in known deafness genes. CONCLUSION These results suggest a potential high prevalence of MYO6 variants in Austrian cases of AD HL. The presence of multiple rare HL variants in some patients highlights the relevance of considering multiple-hit diagnoses for genetic counseling and targeted therapy design.
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Affiliation(s)
- Alexandra Frohne
- Department of Otorhinolaryngology, Head and Neck Surgery
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology
| | | | | | - Franco Laccone
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Juergen Neesen
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | | | - Christian Schoefer
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology
| | - Trevor Lucas
- Department for Cell and Developmental Biology, Center for Anatomy and Cell Biology
| | - Klemens Frei
- Department of Otorhinolaryngology, Head and Neck Surgery
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40
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Panigrahi I, Kumari D, Kumar BNA. Single gene variants causing deafness in Asian Indians. J Genet 2021. [DOI: 10.1007/s12041-021-01288-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
BACKGROUND Hearing loss (HL) is a heterogeneous condition that causes partial or complete hearing impairment. Hundreds of variants in more than 60 genes have been reported to be associated with Hereditary HL (HHL). The HHL prevalence is thought to be high in the Arab population; however, the genetic epidemiology of HHL among Arab populations is understudied. This study aimed to systematically analyze the genetic epidemiology of HHL in Arab countries. METHODS We searched four literature databases (PubMed, Scopus, Science Direct, and Web of Science) from the time of inception until January 2019 using broad search terms to capture all the reported epidemiological and genetic data related to Arab patients with HHL. FINDINGS A total of 2,600 citations were obtained; 96 studies met our inclusion criteria. Our search strategy yielded 121,276 individuals who were tested for HL over 52 years (1966-2018), of whom 8,099 were clinically diagnosed with HL and belonged to 16 Arab countries. A total of 5,394 patients and 61 families with HHL were genotyped, of whom 336 patients and 6 families carried 104 variants in 44 genes and were from 17/22 Arab countries. Of these variants, 72 (in 41 genes) were distinctive to Arab patients. Arab patients manifested distinctive clinical phenotypes. The incidence of HHL in the captured studies ranged from 1.20 to 18 per 1,000 births per year, and the prevalence was the highest in Iraq (76.3%) and the lowest in Jordan (1.5%). INTERPRETATION This is the first systematic review to capture the prevalence and spectrum of variants associated with HHL in an Arab population. There appears to be a distinctive clinical picture for Arab patients with HHL, and the range and distribution of variants among Arab patients differ from those noted in other affected ethnic groups.
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Li Y, Su J, Zhang J, Pei J, Li D, Zhang Y, Li J, Chen M, Zhu B. Targeted next-generation sequencing of deaf patients from Southwestern China. Mol Genet Genomic Med 2021; 9:e1660. [PMID: 33724713 PMCID: PMC8123756 DOI: 10.1002/mgg3.1660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Targeted next-generation sequencing is an efficient tool to identify pathogenic mutations of hereditary deafness. The molecular pathology of deaf patients in southwestern China is not fully understood. METHODS In this study, targeted next-generation sequencing of 127 deafness genes was performed on 84 deaf patients. They were not caused by common mutations of GJB2 gene, including c.35delG, c.109 G>A, c.167delT, c.176_191del16, c.235delC and c.299_300delAT. RESULTS In the cohorts of 84 deaf patients, we did not find any candidate pathogenic variants in 14 deaf patients (16.7%, 14/84). In other 70 deaf patients (83.3%, 70/84), candidate pathogenic variants were identified in 34 genes. Of these 70 deaf patients, the percentage of "Solved" and "Unsolved" patients was 51.43% (36/70) and 48.57% (34/70), respectively. The most common causative genes were SLC26A4 (12.9%, 9/70), MT-RNR1 (11.4%, 8/70), and MYO7A (2.9%, 2/70) in deaf patients. In "Unsolved" patients, possible pathogenic variants were most found in SLC26A4 (8.9%, 3/34), MYO7A (5.9%, 2/34), OTOF (5.9%, 2/34), and PDZD7 (5.9%, 2/34) genes. Interesting, several novel recessive pathogenic variants were identified, like SLC26A4 c.290T>G, SLC26A4 c.599A>G, PDZD7c.490 C>T, etc. CONCLUSION: In addition to common deafness genes, like GJB2, SLC26A4, and MT-RNR1 genes, other deafness genes (MYO7A, OTOF, PDZD7, etc.) were identified in deaf patients from southwestern China. Therefore, the spectrum of deafness genes in this area should be further studied.
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Affiliation(s)
- Yunlong Li
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Jie Su
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jingman Zhang
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jiahong Pei
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Dongmei Li
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Yinhong Zhang
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Jingyu Li
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Menglang Chen
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Baosheng Zhu
- Department of Medical Genetics, First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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Eckert MA, Harris KC, Lang H, Lewis MA, Schmiedt RA, Schulte BA, Steel KP, Vaden KI, Dubno JR. Translational and interdisciplinary insights into presbyacusis: A multidimensional disease. Hear Res 2021; 402:108109. [PMID: 33189490 PMCID: PMC7927149 DOI: 10.1016/j.heares.2020.108109] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 12/18/2022]
Abstract
There are multiple etiologies and phenotypes of age-related hearing loss or presbyacusis. In this review we summarize findings from animal and human studies of presbyacusis, including those that provide the theoretical framework for distinct metabolic, sensory, and neural presbyacusis phenotypes. A key finding in quiet-aged animals is a decline in the endocochlear potential (EP) that results in elevated pure-tone thresholds across frequencies with greater losses at higher frequencies. In contrast, sensory presbyacusis appears to derive, in part, from acute and cumulative effects on hair cells of a lifetime of environmental exposures (e.g., noise), which often result in pronounced high frequency hearing loss. These patterns of hearing loss in animals are recognizable in the human audiogram and can be classified into metabolic and sensory presbyacusis phenotypes, as well as a mixed metabolic+sensory phenotype. However, the audiogram does not fully characterize age-related changes in auditory function. Along with the effects of peripheral auditory system declines on the auditory nerve, primary degeneration in the spiral ganglion also appears to contribute to central auditory system aging. These inner ear alterations often correlate with structural and functional changes throughout the central nervous system and may explain suprathreshold speech communication difficulties in older adults with hearing loss. Throughout this review we highlight potential methods and research directions, with the goal of advancing our understanding, prevention, diagnosis, and treatment of presbyacusis.
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Affiliation(s)
- Mark A Eckert
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA.
| | - Kelly C Harris
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Hainan Lang
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, SC 29425, USA
| | - Morag A Lewis
- King's College London, Wolfson Centre for Age-Related Diseases, London SE1 1UL, United Kingdom
| | - Richard A Schmiedt
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Bradley A Schulte
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, SC 29425, USA; Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Karen P Steel
- King's College London, Wolfson Centre for Age-Related Diseases, London SE1 1UL, United Kingdom
| | - Kenneth I Vaden
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Judy R Dubno
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA; Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, SC 29425, USA
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Wonkam-Tingang E, Schrauwen I, Esoh KK, Bharadwaj T, Nouel-Saied LM, Acharya A, Nasir A, Leal SM, Wonkam A. A novel variant in DMXL2 gene is associated with autosomal dominant non-syndromic hearing impairment (DFNA71) in a Cameroonian family. Exp Biol Med (Maywood) 2021; 246:1524-1532. [PMID: 33715530 DOI: 10.1177/1535370221999746] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Approximately half of congenital hearing impairment cases are inherited, with non-syndromic hearing impairment (NSHI) being the most frequent clinical entity of genetic hearing impairment cases. A family from Cameroon with NSHI was investigated by performing exome sequencing using DNA samples obtained from three family members, followed by direct Sanger sequencing in additional family members and controls participants. We identified an autosomal dominantly inherited novel missense variant [NM_001174116.2:c.918G>T; p.(Q306H)] in DMXL2 gene (MIM:612186) that co-segregates with mild to profound non-syndromic sensorineural hearing impairment . The p.(Q306H) variant which substitutes a highly conserved glutamine residue is predicted deleterious by various bioinformatics tools and is absent from several genome databases. This variant was also neither found in 121 apparently healthy controls without a family history of hearing impairment , nor 112 sporadic NSHI cases from Cameroon. There is one previous report of a large Han Chinese NSHI family that segregates a missense variant in DMXL2. The present study provides additional evidence that DMXL2 is involved in hearing impairment etiology, and we suggest DMXL2 should be considered in diagnostic hearing impairment panels.
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Affiliation(s)
- Edmond Wonkam-Tingang
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Kevin K Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Thashi Bharadwaj
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Liz M Nouel-Saied
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Abdul Nasir
- Synthetic Protein Engineering Lab (SPEL), Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea
| | - Suzanne M Leal
- Center for Statistical Genetics, Sergievsky Center, Taub Institute for Alzheimer's Disease and the Aging Brain, and the Department of Neurology, Columbia University Medical Centre, New York, NY 10032, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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Spectrum of MYO7A Mutations in an Indigenous South African Population Further Elucidates the Nonsyndromic Autosomal Recessive Phenotype of DFNB2 to Include Both Homozygous and Compound Heterozygous Mutations. Genes (Basel) 2021; 12:genes12020274. [PMID: 33671976 PMCID: PMC7919343 DOI: 10.3390/genes12020274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/17/2022] Open
Abstract
MYO7A gene encodes unconventional myosin VIIA, which, when mutated, causes a phenotypic spectrum ranging from recessive hearing loss DFNB2 to deaf-blindness, Usher Type 1B (USH1B). MYO7A mutations are reported in nine DFNB2 families to date, none from sub-Saharan Africa.In DNA, from a cohort of 94 individuals representing 92 families from the Limpopo province of South Africa, eight MYO7A variations were detected among 10 individuals. Family studies identified homozygous and compound heterozygous mutations in 17 individuals out of 32 available family members. Four mutations were novel, p.Gly329Asp, p.Arg373His, p.Tyr1780Ser, and p.Pro2126Leufs*5. Two variations, p.Ser617Pro and p.Thr381Met, previously listed as of uncertain significance (ClinVar), were confirmed to be pathogenic. The identified mutations are predicted to interfere with the conformational properties of myosin VIIA through interruption or abrogation of multiple interactions between the mutant and neighbouring residues. Specifically, p.Pro2126Leufs*5, is predicted to abolish the critical site for the interactions between the tail and the motor domain essential for the autoregulation, leaving a non-functional, unregulated protein that causes hearing loss. We have identified MYO7A as a possible key deafness gene among indigenous sub-Saharan Africans. The spectrum of MYO7A mutations in this South African population points to DFNB2 as a specific entity that may occur in a homozygous or in a compound heterozygous state.
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Wonkam A, Lebeko K, Mowla S, Noubiap JJ, Chong M, Pare G. Whole exome sequencing reveals a biallelic frameshift mutation in GRXCR2 in hearing impairment in Cameroon. Mol Genet Genomic Med 2021; 9:e1609. [PMID: 33528103 PMCID: PMC8104159 DOI: 10.1002/mgg3.1609] [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: 11/11/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hearing impairment (HI) genes are poorly studied in African populations. METHODS We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 10 individuals with HI, from four multiplex families from Cameroon, two of which were previously unresolved with a targeted gene enrichment (TGE) panel of 116 genes. In silico protein modelling, western blotting and live imaging of transfected HEK293 cells were performed to study protein structure and functions. RESULTS All PLP variants previously identified with TGE were replicated. In one previously unresolved family, we found a homozygous frameshift PLP variant in GRXCR2 (OMIM: 615762), NM_001080516.1(GRXCR2):c.251delC p.(Ile85SerfsTer33), in two affected siblings; and additionally, in 1/80 unrelated individuals affected with non-syndromic hearing impairment (NSHI). The GRXCR2-c.251delC variant introduced a premature stop codon, leading to truncation and loss of a zinc-finger domain. Fluorescence confocal microscopy tracked the wild-type GRXCR2 protein to the cellular membrane, unlike the mutated GRXCR2 protein. CONCLUSION This study confirms GRXCR2 as a HI-associated gene. GRXCR2 should be included to the currently available TGE panels for HI diagnosis.
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Affiliation(s)
- Ambroise Wonkam
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kamogelo Lebeko
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaheen Mowla
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Mike Chong
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Guillaume Pare
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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Souissi A, Ben Said M, Ben Ayed I, Elloumi I, Bouzid A, Mosrati MA, Hasnaoui M, Belcadhi M, Idriss N, Kamoun H, Gharbi N, Gibriel AA, Tlili A, Masmoudi S. Novel pathogenic mutations and further evidence for clinical relevance of genes and variants causing hearing impairment in Tunisian population. J Adv Res 2021; 31:13-24. [PMID: 34194829 PMCID: PMC8240103 DOI: 10.1016/j.jare.2021.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/14/2020] [Accepted: 01/07/2021] [Indexed: 12/22/2022] Open
Abstract
Introduction Hearing impairment (HI) is characterized by complex genetic heterogeneity. The evolution of next generation sequencing, including targeted enrichment panels, has revolutionized HI diagnosis. Objectives In this study, we investigated genetic causes in 22 individuals with non-GJB2 HI. Methods We customized a HaloplexHS kit to include 30 genes known to be associated with autosomal recessive nonsyndromic HI (ARNSHI) and Usher syndrome in North Africa. Results In accordance with the ACMG/AMP guidelines, we report 11 pathogenic variants; as follows; five novel variants including three missense (ESRRB-Tyr295Cys, MYO15A-Phe2089Leu and MYO7A-Tyr560Cys) and two nonsense (USH1C-Gln122Ter and CIB2-Arg104Ter) mutations; two previously reported mutations (OTOF-Glu57Ter and PNPT1-Glu475Gly), but first time identified among Tunisian families; and four other identified mutations namely WHRN-Gly808AspfsX11, SLC22A4-Cys113Tyr and two MYO7A compound heterozygous splice site variants that were previously described in Tunisia. Pathogenic variants in WHRN and CIB2 genes, in patients with convincing phenotype ruling out retinitis pigmentosa, provide strong evidence supporting their association with ARNSHI. Moreover, we shed lights on the pathogenic implication of mutations in PNPT1 gene in auditory function providing new evidence for its association with ARNSHI. Lack of segregation of a previously identified causal mutation OTOA-Val603Phe further supports its classification as variant of unknown significance. Our study reports absence of otoacoustic emission in subjects using bilateral hearing aids for several years indicating the importance of screening genetic alteration in OTOF gene for proper management of those patients. Conclusion In conclusion, our findings do not only expand the spectrum of HI mutations in Tunisian patients, but also improve our knowledge about clinical relevance of HI causing genes and variants.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mariem Ben Said
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Ikhlas Ben Ayed
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Ines Elloumi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mohamed Ali Mosrati
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Mehdi Hasnaoui
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Malek Belcadhi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
| | - Nabil Idriss
- Department of Otorhinolaryngology, Taher Sfar University Hospital of Mahdia, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Nourhene Gharbi
- Medical Genetic Department, University Hedi Chaker Hospital of Sfax, Tunisia
- Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Abdullah A. Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy. The British University in Egypt (BUE) Cairo, Egypt
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Tunisia
- Corresponding author at: Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, Sidi Mansour road Km 6, BP “1177”, 3018 Sfax, Tunisia.
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Oluwole OG, Esoh KK, Wonkam-Tingang E, Manyisa N, Noubiap JJ, Chimusa ER, Wonkam A. Whole exome sequencing identifies rare coding variants in novel human-mouse ortholog genes in African individuals diagnosed with non-syndromic hearing impairment. Exp Biol Med (Maywood) 2021; 246:197-206. [PMID: 32996353 PMCID: PMC7871117 DOI: 10.1177/1535370220960388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/28/2020] [Indexed: 01/08/2023] Open
Abstract
Physiologically, the human and murine hearing systems are very similar, justifying the extensive use of mice in experimental models for hearing impairment (HI). About 340 murine HI genes have been reported; however, whether variants in all human-mouse ortholog genes contribute to HI has been rarely investigated. In humans, nearly 120 HI genes have been identified to date, with GJB2 and GJB6 variants accounting for half of congenital HI cases, of genetic origin, in populations of European and Asian ancestries, but not in most African populations. The contribution of variants in other known genes of HI among the populations of African ancestry is poorly studied and displays the lowest pick-up rate. We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 34 novel human-mouse orthologs HI genes, in 40 individuals from Cameroon and South Africa diagnosed with non-syndromic hearing impairment (NSHI), and compared the data to WES data of 129 ethnically matched controls. In addition, protein modeling for selected PLP gene variants, gene enrichment, and network analyses were performed. A total of 4/38 murine genes, d6wsu163e, zfp719, grp152 and minar2, had no human orthologs. WES identified three rare PLP variants in 3/34 human-mouse orthologs genes in three unrelated Cameroonian patients, namely: OCM2, c.227G>C p.(Arg76Thr) and LRGI1, c.1657G>A p.(Gly533Arg) in a heterozygous state, and a PLP variant MCPH1, c.2311C>G p.(Pro771Ala) in a homozygous state. In silico functional analyses suggest that these human-mouse ortholog genes functionally co-expressed interactions with well-established HI genes: GJB2 and GJB6. The study found one homozygous variant in MCPH1, likely to explain HI in one patient, and suggests that human-mouse ortholog variants could contribute to the understanding of the physiology of hearing in humans.
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Affiliation(s)
- Oluwafemi G Oluwole
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Kevin K Esoh
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Edmond Wonkam-Tingang
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI), University of Adelaide and Royal Adelaide Hospital, Adelaide 5000, Australia
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town 7935, South Africa
- Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
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Ding N, Lee S, Lieber-Kotz M, Yang J, Gao X. Advances in genome editing for genetic hearing loss. Adv Drug Deliv Rev 2021; 168:118-133. [PMID: 32387678 DOI: 10.1016/j.addr.2020.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/27/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023]
Abstract
According to the World Health Organization, hearing loss affects over 466 million people worldwide and is the most common human sensory impairment. It is estimated that genetic factors contribute to the causation of approximately 50% of congenital hearing loss. Yet, curative approaches to reversing or preventing genetic hearing impairment are still limited. The clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR-Cas9) systems enable programmable and targeted gene editing in highly versatile manners and offer new gene therapy strategies for genetic hearing loss. Here, we summarize the most common deafness-associated genes, illustrate recent strategies undertaken by using CRISPR-Cas9 systems for targeted gene editing and further compare the CRISPR strategies to non-CRISPR gene therapies. We also examine the merits of different vehicles and delivery forms of genome editing agents. Lastly, we describe the development of animal models that could facilitate the eventual clinical applications of the CRISPR technology to the treatment of genetic hearing diseases.
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Nisenbaum E, Prentiss S, Yan D, Nourbakhsh A, Smeal M, Holcomb M, Cejas I, Telischi F, Liu XZ. Screening Strategies for Deafness Genes and Functional Outcomes in Cochlear Implant Patients. Otol Neurotol 2021; 42:180-187. [PMID: 33885265 PMCID: PMC9237809 DOI: 10.1097/mao.0000000000002969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To review the current state of knowledge about the influence of specific genetic mutations that cause sensorineural hearing loss (SNHL) on cochlear implant (CI) functional outcomes, and how this knowledge may be integrated into clinical practice. A multistep and sequential population-based genetic algorithm suitable for the identification of congenital SNHL mutations before CI placement is also examined. DATA SOURCES, STUDY SELECTION A review was performed of the English literature from 2000 to 2019 using PubMed regarding the influence of specific mutations on CI outcomes and the use of next-generation sequencing for genetic screening of CI patients. CONCLUSION CI is an effective habilitation option for patients with severe-profound congenital SNHL. However, it is well known that CI outcomes show substantial inter-patient variation. Recent advances in genetic studies have improved our understanding of genotype-phenotype relationships for many of the mutations underlying congenital SNHL, and have explored how these relationships may account for some of the variance seen in CI performance outcomes. A sequential genetic screening strategy utilizing next-generation sequencing-based population-specific gene panels may allow for more efficient mutation identification before CI placement. Understanding the relationships between specific mutations and CI outcomes along with integrating routine comprehensive genetic testing into pre-CI evaluations will allow for more effective patient counseling and open the door for the development of mutation-specific treatment strategies.
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Affiliation(s)
- Eric Nisenbaum
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Sandra Prentiss
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Molly Smeal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Meredith Holcomb
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Ivette Cejas
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Fred Telischi
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
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