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Tlili A, Mahfood M, Al Mutery A, Chouchen J. Genetic analysis of 106 sporadic cases with hearing loss in the UAE population. Hum Genomics 2024; 18:59. [PMID: 38844983 PMCID: PMC11157727 DOI: 10.1186/s40246-024-00630-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Hereditary hearing loss is a rare hereditary condition that has a significant presence in consanguineous populations. Despite its prevalence, hearing loss is marked by substantial genetic diversity, which poses challenges for diagnosis and screening, particularly in cases with no clear family history or when the impact of the genetic variant requires functional analysis, such as in the case of missense mutations and UTR variants. The advent of next-generation sequencing (NGS) has transformed the identification of genes and variants linked to various conditions, including hearing loss. However, there remains a high proportion of undiagnosed patients, attributable to various factors, including limitations in sequencing coverage and gaps in our knowledge of the entire genome, among other factors. In this study, our objective was to comprehensively identify the spectrum of genes and variants associated with hearing loss in a cohort of 106 affected individuals from the UAE. RESULTS In this study, we investigated 106 sporadic cases of hearing impairment and performed genetic analyses to identify causative mutations. Screening of the GJB2 gene in these cases revealed its involvement in 24 affected individuals, with specific mutations identified. For individuals without GJB2 mutations, whole exome sequencing (WES) was conducted. WES revealed 33 genetic variants, including 6 homozygous and 27 heterozygous DNA changes, two of which were previously implicated in hearing loss, while 25 variants were novel. We also observed multiple potential pathogenic heterozygous variants across different genes in some cases. Notably, a significant proportion of cases remained without potential pathogenic variants. CONCLUSIONS Our findings confirm the complex genetic landscape of hearing loss and the limitations of WES in achieving a 100% diagnostic rate, especially in conditions characterized by genetic heterogeneity. These results contribute to our understanding of the genetic basis of hearing loss and emphasize the need for further research and comprehensive genetic analyses to elucidate the underlying causes of this condition.
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Affiliation(s)
- Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates.
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates.
| | - Mona Mahfood
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates
| | - Abdullah Al Mutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Building W8 Room 107, P.O. Box: 27272, Sharjah, United Arab Emirates
| | - Jihen Chouchen
- Human Genetics and Stem Cell Laboratory, Research Institute of Sciences and Engineering, University of Sharjah, Sharjah, United Arab Emirates
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Tisi A, Palaniappan S, Maccarrone M. Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease. Biomolecules 2023; 13:1534. [PMID: 37892216 PMCID: PMC10605747 DOI: 10.3390/biom13101534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.
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Affiliation(s)
- Annamaria Tisi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Sakthimala Palaniappan
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Laboratory of Lipid Neurochemistry, European Center for Brain Research (CERC), Santa Lucia Foundation IRCCS, 00143 Rome, Italy
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3
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Ford CL, Riggs WJ, Quigley T, Keifer OP, Whitton JP, Valayannopoulos V. The natural history, clinical outcomes, and genotype-phenotype relationship of otoferlin-related hearing loss: a systematic, quantitative literature review. Hum Genet 2023; 142:1429-1449. [PMID: 37679651 PMCID: PMC10511631 DOI: 10.1007/s00439-023-02595-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023]
Abstract
Congenital hearing loss affects one in 500 newborns. Sequence variations in OTOF, which encodes the calcium-binding protein otoferlin, are responsible for 1-8% of congenital, nonsyndromic hearing loss and are the leading cause of auditory neuropathy spectrum disorders. The natural history of otoferlin-related hearing loss, the relationship between OTOF genotype and hearing loss phenotype, and the outcomes of clinical practices in patients with this genetic disorder are incompletely understood because most analyses have reported on small numbers of cases with homogeneous OTOF genotypes. Here, we present the first systematic, quantitative literature review of otoferlin-related hearing loss, which analyzes patient-specific data from 422 individuals across 61 publications. While most patients display a typical phenotype of severe-to-profound hearing loss with prelingual onset, 10-15% of patients display atypical phenotypes, including mild-to-moderate, progressive, and temperature-sensitive hearing loss. Patients' phenotypic presentations appear to depend on their specific genotypes. For example, non-truncating variants located in and immediately downstream of the C2E calcium-binding domain are more likely to produce atypical phenotypes. Additionally, the prevalence of certain sequence variants and their associated phenotypes varies between populations due to evolutionary founder effects. Our analyses also suggest otoacoustic emissions are less common in older patients and those with two truncating OTOF variants. Critically, our review has implications for the application and limitations of clinical practices, including newborn hearing screenings, hearing aid trials, cochlear implants, and upcoming gene therapy clinical trials. We conclude by discussing the limitations of available research and recommendations for future studies on this genetic cause of hearing loss.
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Hausrat TJ, Vogl C, Neef J, Schweizer M, Yee BK, Strenzke N, Kneussel M. Monoallelic loss of the F-actin-binding protein radixin facilitates startle reactivity and pre-pulse inhibition in mice. Front Cell Dev Biol 2022; 10:987691. [DOI: 10.3389/fcell.2022.987691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
Hearing impairment is one of the most common disorders with a global burden and increasing prevalence in an ever-aging population. Previous research has largely focused on peripheral sensory perception, while the brain circuits of auditory processing and integration remain poorly understood. Mutations in the rdx gene, encoding the F-actin binding protein radixin (Rdx), can induce hearing loss in human patients and homozygous depletion of Rdx causes deafness in mice. However, the precise physiological function of Rdx in hearing and auditory information processing is still ill-defined. Here, we investigated consequences of rdx monoallelic loss in the mouse. Unlike the homozygous (−/−) rdx knockout, which is characterized by the degeneration of actin-based stereocilia and subsequent hearing loss, our analysis of heterozygous (+/−) mutants has revealed a different phenotype. Specifically, monoallelic loss of rdx potentiated the startle reflex in response to acoustic stimulation of increasing intensities, suggesting a gain of function relative to wildtype littermates. The monoallelic loss of the rdx gene also facilitated pre-pulse inhibition of the acoustic startle reflex induced by weak auditory pre-pulse stimuli, indicating a modification to the circuit underlying sensorimotor gating of auditory input. However, the auditory brainstem response (ABR)-based hearing thresholds revealed a mild impairment in peripheral sound perception in rdx (+/-) mice, suggesting minor aberration of stereocilia structural integrity. Taken together, our data suggest a critical role of Rdx in the top-down processing and/or integration of auditory signals, and therefore a novel perspective to uncover further Rdx-mediated mechanisms in central auditory information processing.
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Fu Y, Huang S, Gao X, Han M, Wang G, Kang D, Yuan Y, Dai P. Analysis of the genotype–phenotype correlation of MYO15A variants in Chinese non-syndromic hearing loss patients. BMC Med Genomics 2022; 15:71. [PMID: 35346193 PMCID: PMC8962197 DOI: 10.1186/s12920-022-01201-3] [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: 10/15/2021] [Accepted: 02/28/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Mutations in the MYO15A gene are a widely recognized cause of autosomal recessive non-syndromic sensorineural hearing loss (NSHL) globally. Here, we examined the role and the genotype–phenotype correlation of MYO15A variants in a cohort of Chinese NSHL cases.
Methods
Eighty-one cases with evidenced MYO15A variants from the 2263 Chinese NSHL cases, who underwent next-generation sequencing (NGS), were enrolled in the study. We investigated the association of MYO15A variants with the severity, progression and age of onset of hearing loss, as well as compared it to the previous reports in different nationalities. The cases were divided into groups according to the number of truncating variants: 2 truncating, 1 truncating and 1 non-truncating, 2 non-truncating variants, and compared the severity of HL among the groups.
Results
MYO15A accounted for 3.58% (81/2263) of all NSHL cases. We analyzed 81 MYO15A-related NSHL cases, 73 of whom were with congenital bilateral, symmetric or severe-to-profound hearing loss (HL), however, 2 of them had a postlingual, asymmetric, mild or moderate HL. There were 102 variants identified in all MYO15A structural domains, 76.47% (78/102) of whom were novel. The most common types of detected variants were missense (44/102, 43.14%), followed by frameshift (27/102, 26.47%), nonsense (14/102, 13.72%), splice site (10/102, 9.80%), in frame (4/102, 3.92%), non-coding (2/102, 1.96%) and synonymous (1/102, 0.98%). The most recurrent variant c.10245_10247delCTC was detected in 12 cases. We observed that the MYO15A variants, located in its N-terminal, motor and FERM domains, led to partial deafness with better residual hearing at low frequencies. There were 34 cases with biallelic truncating variants, 37 cases with monoallelic truncating variants, and 13 cases with biallelic non-truncating variants. The biallelic non-truncating variants group had the least number of cases (12/81), and most of them (10/12) were with profound NSHL.
Conclusions
MYO15A is a major gene responsible for NSHL in China. Cases with MYO15A variants mostly showed early-onset, symmetric, severe-to-profound hearing loss. This study is by far the largest focused on the evaluation of the genotype–phenotype correlations among the variants in the MYO15A gene and its implication in the outcome of NSHL. The biallelic non-truncating MYO15A variants commonly caused profound HL, and the cases with one or two truncating MYO15A variants tended to increase the risk of HL. Nevertheless, further investigations are needed to clarify the causes for the variable severities and progression rates of hearing loss and the detected MYO15A variants in these cases.
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Na G, Choi HJ, Joo SY, Rim JH, Kim JA, Kim HY, Yu S, Jeong Y, Shin GC, Noh HE, Lee HY, Kim DH, Gee HY, Jung J, Choi JY. Heterogeneity of MYO15A variants significantly determine the feasibility of acoustic stimulation with hearing aid and cochlear implant. Hear Res 2021; 404:108227. [PMID: 33784549 DOI: 10.1016/j.heares.2021.108227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/15/2022]
Abstract
Autosomal recessive nonsyndromic hearing loss 3 (DFNB3) mainly leads to congenital and severe-to-profound hearing impairment, which is caused by variants in MYO15A. However, audiological heterogeneity in patients with DFNB3 hinders precision medicine in hearing rehabilitation. Here, we aimed to elucidate the heterogeneity of the auditory phenotypes of MYO15A variants according to the affected domain and the feasibilities for acoustic stimulation. We conducted whole-exome sequencing for 10 unrelated individuals from seven multiplex families with DFNB3; 11 MYO15A variants, including the novel frameshift c.900delT (p.Pro301Argfs*143) and nonsense c.4879G > T (p.Glu1627*) variants, were identified. In seven probands, residual hearing at low frequencies was significantly higher in the groups with one or two N-terminal frameshift variants in trans conformation compared to that in the group without these variants. This is consistent with the 56 individuals from the previously published reports that carried a varying number of N-terminal truncating variants in MYO15A. In addition, patients with missense variants in the second FERM domain had better hearing at low frequencies than patients without these variants. Subsequently, acoustic stimulation provided by devices such as hearing aids or cochlear implants was feasible in patients with one or two N-terminal truncating variants or a second FERM missense variant. In conclusion, N-terminal or second FERM variants in MYO15A allow the practical use of acoustic stimulation through hearing aids or electroacoustic stimulation for aural rehabilitation.
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Affiliation(s)
- Gina Na
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Department of Otorhinolaryngology, Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Republic of Korea
| | - Hye Ji Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
| | - Sun Young Joo
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea
| | - John Hoon Rim
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea
| | - Jung Ah Kim
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea
| | - Hye-Youn Kim
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea
| | - Seyoung Yu
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea
| | - Yeonsu Jeong
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
| | - Geun Cheol Shin
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
| | - Hae Eun Noh
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
| | - Ho Young Lee
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
| | - Da Hye Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
| | - Heon Yung Gee
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea.
| | - Jinsei Jung
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea; Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine Seoul, Republic of Korea.
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seoul, Seodaemun-gu 03722, Republic of Korea
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Coez A, Fillon L, Saitovitch A, Rutten C, Marlin S, Boisgontier J, Vinçon-Leite A, Lemaitre H, Grévent D, Roux CJ, Dangouloff-Ros V, Levy R, Bizaguet E, Rouillon I, Garabédian EN, Denoyelle F, Zilbovicius M, Loundon N, Boddaert N. Arterial spin labeling brain MRI study to evaluate the impact of deafness on cerebral perfusion in 79 children before cochlear implantation. Neuroimage Clin 2020; 29:102510. [PMID: 33369563 PMCID: PMC7777537 DOI: 10.1016/j.nicl.2020.102510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/06/2023]
Abstract
Age at implantation is considered to be a major factor, influencing outcomes after pediatric cochlear implantation. In the absence of acoustic input, it has been proposed that cross-modal reorganization can be detrimental for adaptation to the new electrical input provided by a cochlear implant. Here, through a retrospective study, we aimed to investigate differences in cerebral blood flow (CBF) at rest prior to implantation in children with congenital deafness compared to normally hearing children. In addition, we looked at the putative link between pre-operative rest-CBF and the oral intelligibility scores at 12 months post-implantation. Finally, we observed the evolution of perfusion with age, within brain areas showing abnormal rest-CBF associated to deafness, in deaf children and in normally hearing children. In children older than 5 years old, results showed a significant bilateral hypoperfusion in temporal regions in deaf children, particularly in Heschl's gyrus, and a significant hyperperfusion of occipital regions. Furthermore, in children older than 5 years old, whole brain voxel-by-voxel correlation analysis between pre-operative rest-CBF and oral intelligibility scores at 12 months post-implantation, showed significant negative correlation localized in the occipital regions: children who performed worse in the speech perception test one year after implantation were those presenting higher preoperative CBF values in these occipital regions. Finally, when comparing mean relative perfusion (extracted from the temporal regions found abnormal on whole-brain voxel-based analysis) across ages in patients and controls, we observed that the temporal perfusion evolution was significantly different in deaf children than in normally hearing children. Indeed, while temporal perfusion increased with age in normally hearing children, it remained stable in deaf children. We showed a critical period around 4 years old, where in the context of auditory deprivation, there is a lack of synaptic activity in auditory regions. These results support the benefits of early cochlear implantation to maximize the effectiveness of auditory rehabilitation and to avoid cross-modal reorganization.
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Affiliation(s)
- Arnaud Coez
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France; Service d'oto-rhino-laryngologie pédiatrique, Centre de Réference des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France; Laboratoire de correction auditive, Bizaguet, Paris, France; Institut de l'Audition, Paris, France.
| | - Ludovic Fillon
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Ana Saitovitch
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Caroline Rutten
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Sandrine Marlin
- Service de Génétique Médicale, Centre de Référence des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France
| | - Jennifer Boisgontier
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Alice Vinçon-Leite
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Hervé Lemaitre
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - David Grévent
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Charles-Joris Roux
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Volodia Dangouloff-Ros
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Raphaël Levy
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France
| | - Eric Bizaguet
- Service d'oto-rhino-laryngologie pédiatrique, Centre de Réference des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France; Laboratoire de correction auditive, Bizaguet, Paris, France
| | - Isabelle Rouillon
- Service d'oto-rhino-laryngologie pédiatrique, Centre de Réference des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France
| | - Eréa Noël Garabédian
- Service d'oto-rhino-laryngologie pédiatrique, Centre de Réference des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France
| | - Françoise Denoyelle
- Service d'oto-rhino-laryngologie pédiatrique, Centre de Réference des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France; Institut de l'Audition, Paris, France
| | - Monica Zilbovicius
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France; INSERM ERL "Developmental Trajectories & Psychiatry", Université Paris Saclay, Ecole Normale Supérieure Paris-Saclay, Université de Paris, CNRS, Centre Borelli, France
| | - Natalie Loundon
- Service d'oto-rhino-laryngologie pédiatrique, Centre de Réference des Surdités Génétiques, Hôpital Necker Enfants Malades, AP-HP, Université de Paris, Paris, France; Institut de l'Audition, Paris, France
| | - Nathalie Boddaert
- Service de radiologie pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris, APHP, Université de Paris, INSERM U1163, Institut Imagine, Paris, France; INSERM ERL "Developmental Trajectories & Psychiatry", Université Paris Saclay, Ecole Normale Supérieure Paris-Saclay, Université de Paris, CNRS, Centre Borelli, France
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Xiang YB, Xu CY, Xu YZ, Li HZ, Zhou LL, Xu XQ, Chen ZH, Tang SH. Next-generation sequencing identifies rare pathogenic and novel candidate variants in a cohort of Chinese patients with syndromic or nonsyndromic hearing loss. Mol Genet Genomic Med 2020; 8:e1539. [PMID: 33095980 PMCID: PMC7767562 DOI: 10.1002/mgg3.1539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/27/2020] [Accepted: 10/02/2020] [Indexed: 11/15/2022] Open
Abstract
Background Hearing loss (HL) is a common sensory disorder in humans characterized by extreme clinical and genetic heterogeneity. In recent years, next‐generation sequencing (NGS) technologies have proven to be highly effective and powerful tools for population genetic studies of HL. Here, we analyzed clinical and molecular data from 21 Chinese deaf families who did not have hotspot mutations in the common deafness genes GJB2, SLC26A4, GJB3, and MT‐RNR1. Method Targeted next‐generation sequencing (TGS) of 127 known deafness genes was performed in probands of 12 families, while whole‐exome sequencing (WES) or trio‐WES was used for the remaining nine families. Results Potential pathogenic mutations in a total of 12 deafness genes were identified in 13 probands; the mutations were observed in GJB2, CDH23, EDNRB, MYO15A, OTOA, OTOF, TBC1D24, SALL1, TMC1, TWNK, USH1C, and USH1G, with eight of the identified mutations being novel. Further, a copy number variant (CNV) was detected in one proband with heterozygous deletion of chromosome 4p16.3‐4p15.32. Thus, the total diagnostic rate using NGS in our deafness patients reached 66.67% (14/21). Conclusions These results expand the mutation spectrum of deafness‐causing genes and provide support for the use of NGS detection technologies for routine molecular diagnosis in Chinese deaf populations.
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Affiliation(s)
- Yan-Bao Xiang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Chen-Yang Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Yun-Zhi Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Huan-Zheng Li
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Li-Li Zhou
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Xue-Qin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China
| | - Zi-Hui Chen
- Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Shao-Hua Tang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, China.,Key laboratory of Medical Genetic, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
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9
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Wu CC, Tsai CY, Lin YH, Chen PY, Lin PH, Cheng YF, Wu CM, Lin YH, Lee CY, Erdenechuluun J, Liu TC, Chen PL, Hsu CJ. Genetic Epidemiology and Clinical Features of Hereditary Hearing Impairment in the Taiwanese Population. Genes (Basel) 2019; 10:genes10100772. [PMID: 31581539 PMCID: PMC6826657 DOI: 10.3390/genes10100772] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/19/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
Hereditary hearing impairment (HHI) is a common but heterogeneous clinical entity caused by mutations in a plethora of deafness genes. Research over the past few decades has shown that the genetic epidemiology of HHI varies significantly across populations. In this study, we used different genetic examination strategies to address the genetic causes of HHI in a large Taiwanese cohort composed of >5000 hearing-impaired families. We also analyzed the clinical features associated with specific genetic mutations. Our results demonstrated that next-generation sequencing-based examination strategies could achieve genetic diagnosis in approximately half of the families. Common deafness-associated genes in the Taiwanese patients assessed, in the order of prevalence, included GJB2, SLC26A4, OTOF, MYO15A, and MTRNR1, which were similar to those found in other populations. However, the Taiwanese patients had some unique mutations in these genes. These findings may have important clinical implications for refining molecular diagnostics, facilitating genetic counseling, and enabling precision medicine for the management of HHI.
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Affiliation(s)
- Chen-Chi Wu
- 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.
| | - Yi-Hsin Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, Taiwan.
| | - Pey-Yu Chen
- Department of Otolaryngology, Mackay Memorial Hospital, Taipei 10449, Taiwan.
| | - Pei-Hsuan Lin
- Department of Otolaryngology, National Taiwan University Hospital Yunlin Branch, Yunlin 64041, Taiwan.
| | - Yen-Fu Cheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan.
- Department of Otolaryngology-Head and Neck Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan.
| | - Che-Ming Wu
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Linkou 33302, Taiwan.
| | - Yin-Hung Lin
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei 10055, Taiwan.
| | - Chee-Yee Lee
- Department of Otolaryngology, Buddhist Tzuchi General Hospital, Taichung Branch, Taichung 42743, Taiwan.
| | - Jargalkhuu Erdenechuluun
- Department of Otolaryngology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia.
- The EMJJ Otolaryngology Hospital, Ulaanbaatar 14210, Mongolia.
- Department of Otolaryngology, National Center for Maternal and Child Health, Ulaanbaatar 16060, Mongolia.
| | - Tien-Chen Liu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei 10002, 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.
| | - 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.
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Bai X, Nian S, Feng L, Ruan Q, Luo X, Wu M, Yan Z. Identification of novel variants in MYO15A, OTOF, and RDX with hearing loss by next-generation sequencing. Mol Genet Genomic Med 2019; 7:e808. [PMID: 31250571 PMCID: PMC6687625 DOI: 10.1002/mgg3.808] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 03/11/2019] [Accepted: 05/17/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Nonsyndromic hearing loss (NSHL) is the most common sensorineural disorder and one of the most common human defects. Autosomal recessive inheritance accounts for a huge percentage of familial cases. Next-generation sequencing (NGS) is a powerful molecular diagnostic strategy for NSHL. The combination of a microarray gene chip and NGS can better delineate the etiology and genetic cause of deafness in many cases. METHODS One hundred and thirty-one unrelated students with NSHL who attend a special education school in Yunnan Province were recruited. Firstly, four common deafness-related genes (GJB2, GJB3, SLC26A4, and mtDNA 12S rRNA) were evaluated for mutations using a microarray kit. Furthermore, 227 known human deafness genes were sequenced to identify the responsible genetic variant of the proband in three Chinese families with autosomal recessive hearing loss. The mutational status of family members of the probands was validated by Sanger sequencing. RESULTS Five novel variants were found in three families using NGS. In family 1, we identified compound heterozygosity at the MYO15A (OMIM, #600316), including an duplication variant c.3866dupC, p.His1290Alafs*25 and a 3-bp deletion (c.10251_10253del, p.Phe3420del), resulting in protein length changes and premature protein truncation, respectively. In family 2, two affected siblings from a consanguineous Chinese Dai family harbored an c.1274G>C, p.Arg425Pro missense variant in the OTOF (OMIM, #601071). In family 3, we identified compound heterozygosity for c.129_130del, p.His43Glnfs*28 and c.76_79del, p.Lys26* in the RDX gene (OMIM, #611022). CONCLUSION Five novel variants were found in three families with NSHL. Our findings extend the mutational spectrum in deafness-related genes and will help physicians in better understanding the etiology of hearing loss.
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Affiliation(s)
- Xuejing Bai
- Department of Laboratory, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, P.R. China
| | - Shiyan Nian
- Department of Laboratory, People's Hospital of Yuxi City, Yuxi, P.R. China
| | - Lei Feng
- Department of Laboratory, People's Hospital of Yuxi City, Yuxi, P.R. China
| | - Qingrong Ruan
- Department of Laboratory, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, P.R. China
| | - Xuan Luo
- Department of Laboratory, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, P.R. China
| | - Mengna Wu
- Department of Laboratory, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, P.R. China
| | - Zefeng Yan
- Department of Laboratory, The Sixth Affiliated Hospital of Kunming Medical University, Yuxi, P.R. China
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